Looking for modules in CD4

Looking at proliferating cells did not identify modules of significance. This further approach will be taken to identify modules across CD4s. I will be omitting those populations strongly associated with annotated CD8+ t cells identified in the annotating proliferation modules file. Those are: Central_memory, Naive_T_3, Naive_T_1, and CD8_TEMRA.

I’m also excluding proliferating, as those cells are likely to drive a proliferation module on their own that won’t be interesting given the parallel analyses.

In this case I’ll be doing similar iterations to what I did previously for the proliferating, but since there are sufficient cells, we’ll look across individuals and merge modules within treatment groups to get insteresting consensus subsets if possible.

As before, I’m checking to see there are sufficient populations to look at. In this case we do have enough to go for the most desirable, treatment + timepoint + participant split.

keep<-c("Treg",     "Polarized_Effector_T", "Exhausted_Th1", "Exhausted_Memory", "Effector_Th1_CD4_and_CD8", "Th2", "CXCR5_Memory",  "Naive_T_2", "Memory_T_1", "Memory_T_2")
results<-subset(results, idents = keep)
## Loading required package: Signac
table(results$Treatment)
## 
##   Bup.Nalo  Methadone Naltrexone 
##       8193       2769       5199
table(results$Timepoint)
## 
##    0    3 
## 9701 6460
table(paste(results$Treatment, results$Timepoint))
## 
##   Bup.Nalo 0   Bup.Nalo 3  Methadone 0  Methadone 3 Naltrexone 0 Naltrexone 3 
##         5302         2891         1105         1664         3294         1905
table(paste(results$Treatment, results$Participant))
## 
##   Bup.Nalo 5014   Bup.Nalo 5017   Bup.Nalo 5018   Bup.Nalo 5023  Methadone 5003 
##            1530            1079            4589             995             424 
##  Methadone 5009  Methadone 5016  Methadone 5020 Naltrexone 5021 Naltrexone 5026 
##             956             748             641             650            1866 
## Naltrexone 5035 Naltrexone 5037 
##            1183            1500
table(paste( results$Timepoint, results$Participant))
## 
## 0 5003 0 5009 0 5014 0 5016 0 5017 0 5018 0 5020 0 5021 0 5023 0 5026 0 5035 
##    199    160    462    327    246   3936    419    239    658   1495    556 
## 0 5037 3 5003 3 5009 3 5014 3 5016 3 5017 3 5018 3 5020 3 5021 3 5023 3 5026 
##   1004    225    796   1068    421    833    653    222    411    337    371 
## 3 5035 3 5037 
##    627    496
results$P_TP<-paste(results$Participant, results$Timepoint, sep="_")

results.split<-SplitObject(results, "P_TP")
#npcs and softpowers, selecting npc based on last nonplataue pc on elbow plot, selecting softpower as first above 0.8 
#repeat 1 
#optional 
#ran this twice, once with the standard criteria (elbow PCs + first softpower > 0.8, selecting a local maxima if 0.8 not exceeded)
#second time is replacing the softpower of the ones that dont id 3 modules at least with a softpower one lower unitl we get at least 3  (min softpower 4)
#repeated - 1, 4, 8, 11 (5021_0), 12, 15, 16, 18, 24
#commented this one out to acclerate stitching 
#conds<-cbind(c(6,6,6,6,7,7,7,6,3, 6, 3, 5, 6,5,6,4, 4,4, 6, 7,5,5,6, 5) ,c(12,4,8,8,4,6,6,10,5,8,12,10,7,10,10,16, 8,16,3,8,8,3,8, 10))
#mods1<-WrapGroupModID(results.split, "NA", conds)

conds<-cbind(c(6,6,6,6,7,7,7,6,3, 6, 3, 5, 6,5,6,4, 4,4, 6, 7,5,5,6, 5 ) ,
             c(5,4,8,5,4,6,6,9,5,8,7,9,7,10, 8, 7, 8,8,3,8,8,3,8, 6))
mods1<-WrapGroupModID(results.split, "NA", conds)
## [1] "5018_0"
## PC_ 1 
## Positive:  ZEB2, AOAH, VCAN, IGKC, HDAC9, GNLY, NKG7, CCL5, PID1, ACTB 
##     CCSER1, TCF7L2, AUTS2, AC243829.2, TMSB10, PIP5K1B, VAV3, C1orf21, KCNQ5, ST6GALNAC3 
## Negative:  INPP4B, CAMK4, PAG1, SERINC5, TTC39C, CASK, CDC14A, HIVEP2, RORA, ARHGAP15 
##     ANK3, TNIK, TNFAIP8, MDFIC, LEF1, SKAP1, DOCK10, ITGB1, KLF12, RASGRF2 
## PC_ 2 
## Positive:  LINC02694, IKZF2, AC013652.1, TTN, AC093865.1, CDHR3, RTKN2, STAM, CCDC141, TOX 
##     DUSP4, CTLA4, IL2RA, HPGD, ST8SIA6, F5, FANK1, TSHR, MCF2L2, ADAM12 
## Negative:  ANK3, NELL2, RASGRF2, NR3C2, THEMIS, IFNG-AS1, ITGA4, SBF2, AC139720.1, DPP4 
##     PLCB1, BCL2, BTBD11, MYBL1, TAFA1, INPP4B, UST, RBMS1, SATB1-AS1, PRKN 
## PC_ 3 
## Positive:  TGFBR3, C1orf21, AOAH, PPP2R2B, PDGFD, AC243829.2, ZEB2, AGAP1, NCALD, DTHD1 
##     SYTL2, PARP8, THEMIS, GTDC1, MYBL1, PZP, A2M, LINC02384, SLC4A4, HIVEP3 
## Negative:  LEF1, TSHZ2, PRKCA, FHIT, TXK, SESN3, PLCL1, FAAH2, CMTM8, MAP3K1 
##     SERINC5, KANK1, AL589693.1, AC139720.1, PVT1, LTB, AC233976.1, FAM13A, TIAM1, BCL2 
## PC_ 4 
## Positive:  GCNT4, AL353660.1, ST8SIA1, TOX, LINC01934, RBMS3, SGPP2, IKZF2, LEF1, AC093865.1 
##     TAFA2, SESN3, ITGA4, TXK, SLC14A1, C12orf42, BICDL1, MALAT1, GLCCI1, MAML2 
## Negative:  FRY, ADAM12, PTPN13, PLD1, AL589693.1, ADAM19, LINC00299, RUNX2, CCR6, MCF2L2 
##     COL5A3, B4GALT5, PLCB1, ANTXR2, MB21D2, HLF, ANKRD28, EEPD1, ZNF462, CEP112 
## PC_ 5 
## Positive:  VCAN, ZEB2, PID1, HDAC9, VAV3, TCF7L2, BACH1, PDE4D, MAML3, CCSER1 
##     PCSK5, AOAH, IGF1R, SBF2, JAZF1, PELI2, NRIP1, MAP3K1, S100Z, AUTS2 
## Negative:  ERN1, SLF1, ST8SIA1, LRIG1, GNAO1, ANK3, THEMIS, RORA, KIAA0825, PCAT1 
##     ITGB1, PLEKHA5, ADAM19, BICDL1, INPP4B, IL18R1, DLGAP1, LINC01934, SERINC5, SMC4 
##    Power SFT.R.sq   slope truncated.R.sq  mean.k. median.k.   max.k.
## 1      1 3.70e-01 14.9000          0.894 1.07e+02  1.07e+02 1.13e+02
## 2      2 8.56e-02  2.6200          0.907 5.52e+01  5.51e+01 6.21e+01
## 3      3 4.07e-05 -0.0367          0.820 2.86e+01  2.84e+01 3.45e+01
## 4      4 7.46e-02 -1.1800          0.877 1.49e+01  1.47e+01 1.94e+01
## 5      5 2.11e-01 -1.6500          0.794 7.79e+00  7.60e+00 1.10e+01
## 6      6 3.60e-01 -1.8400          0.731 4.10e+00  3.94e+00 6.34e+00
## 7      7 5.90e-01 -2.3600          0.748 2.17e+00  2.05e+00 3.70e+00
## 8      8 5.40e-01 -2.5000          0.588 1.16e+00  1.07e+00 2.18e+00
## 9      9 6.84e-01 -2.2700          0.765 6.22e-01  5.65e-01 1.30e+00
## 10    10 7.50e-01 -2.5000          0.766 3.36e-01  2.98e-01 7.81e-01
## 11    12 8.87e-01 -2.3000          0.881 1.00e-01  8.55e-02 2.89e-01
## 12    14 9.62e-01 -2.1000          0.954 3.10e-02  2.43e-02 1.10e-01
## 13    16 9.54e-01 -1.9400          0.942 9.90e-03  7.04e-03 4.30e-02
## 14    18 9.43e-01 -1.7100          0.933 3.29e-03  2.08e-03 1.71e-02
## 15    20 2.90e-01 -3.4500          0.171 1.15e-03  6.46e-04 9.17e-03

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5   6 
## 107  29  26  16  11  11  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 7 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $yellow
##  [1] "INPP4B"     "CAMK4"      "PAG1"       "SERINC5"    "TTC39C"    
##  [6] "CASK"       "CDC14A"     "HIVEP2"     "RORA"       "ARHGAP15"  
## [11] "ANK3"       "TNIK"       "TNFAIP8"    "MDFIC"      "LEF1"      
## [16] "SKAP1"      "DOCK10"     "ITGB1"      "KLF12"      "RASGRF2"   
## [21] "SORL1"      "PVT1"       "RUNX1"      "FAAH2"      "PCAT1"     
## [26] "NELL2"      "NR3C2"      "THEMIS"     "ITGA4"      "AC139720.1"
## [31] "DPP4"       "BCL2"       "BTBD11"     "TAFA1"      "UST"       
## [36] "RBMS1"      "SATB1-AS1"  "PRKN"       "MAN1C1"     "LINC01934" 
## [41] "FMN1"       "FKBP5"      "RNF157"     "PARP8"      "TSHZ2"     
## [46] "PRKCA"      "TXK"        "SESN3"      "PLCL1"      "CMTM8"     
## [51] "MAP3K1"     "KANK1"      "AC233976.1" "AL353660.1" "RETREG1"   
## [56] "ST8SIA1"    "MALAT1"     "MAML2"      "MLLT3"      "SPON1"     
## [61] "ADAM19"     "MB21D2"     "GREM2"      "ERN1"       "LRIG1"     
## [66] "SAMD12"    
## 
## $brown
##  [1] "LINC02694"  "IKZF2"      "AC013652.1" "TTN"        "AC093865.1"
##  [6] "CDHR3"      "RTKN2"      "STAM"       "CCDC141"    "TOX"       
## [11] "DUSP4"      "CTLA4"      "IL2RA"      "HPGD"       "ST8SIA6"   
## [16] "F5"         "FANK1"      "TSHR"       "ATXN7L1"    "TAFA2"     
## [21] "MIR181A1HG" "SLC16A10"   "GCNT4"      "RBMS3"      "SGPP2"     
## [26] "SLC14A1"    "GLCCI1"    
## 
## $red
##  [1] "MCF2L2"     "ADAM12"     "AL136456.1" "AL589693.1" "FRY"       
##  [6] "PTPN13"     "RUNX2"      "CCR6"       "ANK1"       "DUSP16"    
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "11/10000 permutations failed the Mann-Whitney test."
## $yellow
##  [1] "INPP4B"     "CAMK4"      "PAG1"       "SERINC5"    "TTC39C"    
##  [6] "CASK"       "CDC14A"     "HIVEP2"     "RORA"       "ARHGAP15"  
## [11] "ANK3"       "TNIK"       "TNFAIP8"    "MDFIC"      "LEF1"      
## [16] "SKAP1"      "DOCK10"     "ITGB1"      "KLF12"      "RASGRF2"   
## [21] "SORL1"      "PVT1"       "RUNX1"      "FAAH2"      "PCAT1"     
## [26] "NELL2"      "NR3C2"      "THEMIS"     "ITGA4"      "AC139720.1"
## [31] "DPP4"       "BCL2"       "BTBD11"     "TAFA1"      "UST"       
## [36] "RBMS1"      "SATB1-AS1"  "PRKN"       "MAN1C1"     "LINC01934" 
## [41] "FMN1"       "FKBP5"      "RNF157"     "PARP8"      "TSHZ2"     
## [46] "PRKCA"      "TXK"        "SESN3"      "PLCL1"      "CMTM8"     
## [51] "MAP3K1"     "KANK1"      "AC233976.1" "AL353660.1" "RETREG1"   
## [56] "ST8SIA1"    "MALAT1"     "MAML2"      "MLLT3"      "SPON1"     
## [61] "ADAM19"     "MB21D2"     "GREM2"      "ERN1"       "LRIG1"     
## [66] "SAMD12"    
## 
## $brown
##  [1] "LINC02694"  "IKZF2"      "AC013652.1" "TTN"        "AC093865.1"
##  [6] "CDHR3"      "RTKN2"      "STAM"       "CCDC141"    "TOX"       
## [11] "DUSP4"      "CTLA4"      "IL2RA"      "HPGD"       "ST8SIA6"   
## [16] "F5"         "FANK1"      "TSHR"       "ATXN7L1"    "TAFA2"     
## [21] "MIR181A1HG" "SLC16A10"   "GCNT4"      "RBMS3"      "SGPP2"     
## [26] "SLC14A1"    "GLCCI1"    
## 
## $red
##  [1] "MCF2L2"     "ADAM12"     "AL136456.1" "AL589693.1" "FRY"       
##  [6] "PTPN13"     "RUNX2"      "CCR6"       "ANK1"       "DUSP16"    
## 
## [1] "5018_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.8401
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50231
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 5.332e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  AC105402.3, RPL41, RPL19, RPS18, RPS19, RPL37A, AOAH, BANK1, NKG7, AC243829.2 
##     CDH4, SPON2, RPL28, GNLY, RPL18A, PRSS23, WDFY4, AL450352.1, C1orf21, RPS28 
## Negative:  ARHGAP15, PAG1, DPYD, MBNL1, RORA, CNOT6L, LINC01619, KLF12, ANTXR2, GNAQ 
##     PPP3CA, GPRIN3, PARP8, ZBTB20, RBMS1, CDC14A, SKAP1, GLS, FBXL17, TMEM65 
## PC_ 2 
## Positive:  ANK3, MYBL1, THEMIS, RASGRF2, INPP4B, PLCB1, ITGA4, BTBD11, PARP8, BACH2 
##     DPP4, NR3C2, SBF2, RBMS1, PIK3R1, ATP10A, PZP, AOAH, LINC01934, SCML4 
## Negative:  TTN, IKZF2, LINC02694, CCDC141, AC093865.1, STAM, CDHR3, AC013652.1, MIR181A1HG, TAFA2 
##     CENPF, AL136456.1, PALM2-AKAP2, ATXN7L1, F5, RTKN2, ABLIM1, MKI67, TOX, DTL 
## PC_ 3 
## Positive:  ZEB2, AOAH, C1orf21, GNLY, PDGFD, ARHGAP26, ADGRG5, RRM2, AC243829.2, RAD51 
##     CBLB, MCTP2, STMN1, SAMD3, DTHD1, NCAPG, LYN, IL18RAP, PPP2R2B, PLCB1 
## Negative:  TSHZ2, PRKCA, AL589693.1, LEF1, KANK1, CMTM8, PLCL1, FMN1, TIAM1, PAG1 
##     PTPN13, FAAH2, MCF2L2, INPP4B, CDC14A, FRY, AC233976.1, LDLRAD4, SESN3, SAMD12 
## PC_ 4 
## Positive:  LINC02694, CCDC141, AC013652.1, CDHR3, ARHGAP26, IKZF2, HPGD, MIR4435-2HG, ZEB2, C1orf21 
##     AOAH, TTN, AC093865.1, ARL15, TOX, MSC-AS1, STAM, PPP2R2B, DCP1B, NIBAN1 
## Negative:  TOP2A, KIF4A, DIAPH3, STMN1, RAD51, CIT, SGO2, DTL, DLGAP5, RRM2 
##     POLQ, CKAP2L, ESPL1, HJURP, CEP55, AURKA, STIL, HIST1H3B, KIF14, NCAPG 
## PC_ 5 
## Positive:  RPL28, RPL41, RPS28, RPS19, RPS18, TMSB10, EEF1A1, RPL18A, LTB, RPL37A 
##     RPL37, RPL19, IL32, A2M, CR1, AC013652.1, FRY, PLCG2, PZP, GRN 
## Negative:  ST8SIA1, ITGA4, GCNT4, TRPS1, CHN1, PHEX, KIAA1671, AHCYL2, LEF1, UBASH3B 
##     CYP7B1, FHIT, APBA2, VPS54, SGPP2, LINC00598, BCAS3, AL353660.1, BICDL1, L3MBTL4 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k. max.k.
## 1      1   0.0407  -7.60          0.646 113.0000  1.13e+02 119.00
## 2      2   0.3270 -10.30          0.698  58.5000  5.79e+01  66.50
## 3      3   0.5740  -8.53          0.680  30.6000  3.00e+01  39.00
## 4      4   0.7030  -6.90          0.718  16.2000  1.57e+01  24.20
## 5      5   0.3230 -12.40          0.161   8.6900  8.36e+00  16.10
## 6      6   0.3330 -12.20          0.142   4.7400  4.47e+00  11.40
## 7      7   0.3640  -7.46          0.201   2.6500  2.41e+00   8.55
## 8      8   0.3830  -9.35          0.210   1.5100  1.31e+00   6.74
## 9      9   0.3870  -6.72          0.237   0.8900  7.33e-01   5.53
## 10    10   0.3250  -6.16          0.133   0.5420  4.06e-01   4.67
## 11    12   0.3900  -5.25          0.250   0.2260  1.28e-01   3.54
## 12    14   0.3830  -4.84          0.212   0.1110  4.17e-02   2.84
## 13    16   0.3000  -3.81          0.102   0.0646  1.41e-02   2.37
## 14    18   0.3660  -3.68          0.209   0.0427  4.81e-03   2.04
## 15    20   0.3860  -3.41          0.224   0.0312  1.70e-03   1.80

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  0  1  2  3  4  5  6  7  8 
## 13 46 38 37 30 18 15 15 10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
## $turquoise
##  [1] "AC105402.3" "BANK1"      "WDFY4"      "UBE2E2"     "RALGPS2"   
##  [6] "MBNL1"      "RORA"       "LINC01619"  "KLF12"      "PPP3CA"    
## [11] "GPRIN3"     "ZBTB20"     "GLS"        "FBXL17"     "THEMIS"    
## [16] "RASGRF2"    "BTBD11"     "BACH2"      "DPP4"       "NR3C2"     
## [21] "SBF2"       "LYN"        "CR1"        "GRN"        "CRIP2"     
## [26] "KAT2B"      "LINC00299"  "B4GALT5"    "SNX9"       "MB21D2"    
## [31] "TANC2"      "RNF157"     "BLK"        "CDK14"      "EBF1"      
## [36] "USP6NL"     "MEF2C"      "MARCH1"     "HLA-DQA1"   "COBLL1"    
## [41] "PLXDC2"     "TBC1D9"     "PAXBP1-AS1" "FAM49A"     "MTSS1"     
## [46] "LINC00665" 
## 
## $pink
##  [1] "RPL41"  "RPL19"  "RPS19"  "RPL37A" "RPL18A" "RPS28"  "RPL37"  "TMSB10"
##  [9] "LTB"    "IL32"  
## 
## $brown
##  [1] "RPS18"      "RPL28"      "AL450352.1" "PLCG2"      "CENPF"     
##  [6] "MKI67"      "DTL"        "STIL"       "RRM2"       "RAD51"     
## [11] "STMN1"      "NCAPG"      "KIF15"      "CIT"        "TOP2A"     
## [16] "KIF4A"      "DIAPH3"     "SGO2"       "DLGAP5"     "POLQ"      
## [21] "CKAP2L"     "ESPL1"      "HJURP"      "CEP55"      "AURKA"     
## [26] "HIST1H3B"   "KIF14"      "ANLN"       "CDCA2"      "KIF18A"    
## [31] "DEPDC1B"    "SHCBP1"     "EEF1A1"     "LMNA"       "FILIP1L"   
## [36] "GATA3"      "ZBTB16"    
## 
## $red
##  [1] "AOAH"       "NKG7"       "AC243829.2" "GNLY"       "PRSS23"    
##  [6] "C1orf21"    "EPB41L4A"   "PZP"        "A2M"        "ZEB2"      
## [11] "PDGFD"      "ADGRG5"     "DTHD1"      "KLRK1"      "CCL5"      
## 
## $black
##  [1] "SPON2"    "TMCC3"    "MYBL1"    "PLCB1"    "ATP10A"   "IFNG-AS1"
##  [7] "FNDC3B"   "PELI2"    "ARHGAP26" "MCTP2"    "SAMD3"    "IL18RAP" 
## [13] "PPP2R2B"  "L3MBTL4"  "SYTL2"   
## 
## $blue
##  [1] "ARHGAP15"   "PAG1"       "RBMS1"      "CDC14A"     "TMEM65"    
##  [6] "AKT3"       "INPP4B"     "ANK3"       "UST"        "PRKCA"     
## [11] "AL589693.1" "LEF1"       "KANK1"      "CMTM8"      "FMN1"      
## [16] "TIAM1"      "PTPN13"     "FAAH2"      "FRY"        "AC233976.1"
## [21] "SESN3"      "SAMD12"     "AC139720.1" "FHIT"       "RETREG1"   
## [26] "BCL2"       "ST8SIA1"    "GCNT4"      "CHN1"       "PHEX"      
## [31] "VPS54"      "AL353660.1" "BICDL1"     "FAM160A1"   "ADAM19"    
## [36] "CCR6"       "AFF3"       "FCHSD2"    
## 
## $green
##  [1] "DPYD"        "ANTXR2"      "GNAQ"        "SKAP1"       "PAM"        
##  [6] "TTN"         "IKZF2"       "LINC02694"   "CCDC141"     "AC093865.1" 
## [11] "STAM"        "CDHR3"       "AC013652.1"  "MIR181A1HG"  "TAFA2"      
## [16] "AL136456.1"  "PALM2-AKAP2" "ATXN7L1"     "F5"          "RTKN2"      
## [21] "ABLIM1"      "TOX"         "ENTPD1"      "LDLRAD4"     "TSHR"       
## [26] "ADAM12"      "TSHZ2"       "PLCL1"       "MCF2L2"      "ITGB1"      
## [31] "HPGD"        "MIR4435-2HG" "ARL15"       "MSC-AS1"     "DCP1B"      
## [36] "NIBAN1"      "JAZF1"       "ST8SIA6"     "KIAA1671"    "AHCYL2"     
## [41] "UBASH3B"     "CYP7B1"      "SGPP2"       "BCAS3"       "SH3RF3"     
## [46] "CD247"       "RBMS3"       "PLD1"       
## 
## [1] "8840/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "155/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $pink
##  [1] "RPL41"  "RPL19"  "RPS19"  "RPL37A" "RPL18A" "RPS28"  "RPL37"  "TMSB10"
##  [9] "LTB"    "IL32"  
## 
## $brown
##  [1] "RPS18"      "RPL28"      "AL450352.1" "PLCG2"      "CENPF"     
##  [6] "MKI67"      "DTL"        "STIL"       "RRM2"       "RAD51"     
## [11] "STMN1"      "NCAPG"      "KIF15"      "CIT"        "TOP2A"     
## [16] "KIF4A"      "DIAPH3"     "SGO2"       "DLGAP5"     "POLQ"      
## [21] "CKAP2L"     "ESPL1"      "HJURP"      "CEP55"      "AURKA"     
## [26] "HIST1H3B"   "KIF14"      "ANLN"       "CDCA2"      "KIF18A"    
## [31] "DEPDC1B"    "SHCBP1"     "EEF1A1"     "LMNA"       "FILIP1L"   
## [36] "GATA3"      "ZBTB16"    
## 
## $red
##  [1] "AOAH"       "NKG7"       "AC243829.2" "GNLY"       "PRSS23"    
##  [6] "C1orf21"    "EPB41L4A"   "PZP"        "A2M"        "ZEB2"      
## [11] "PDGFD"      "ADGRG5"     "DTHD1"      "KLRK1"      "CCL5"      
## 
## $black
##  [1] "SPON2"    "TMCC3"    "MYBL1"    "PLCB1"    "ATP10A"   "IFNG-AS1"
##  [7] "FNDC3B"   "PELI2"    "ARHGAP26" "MCTP2"    "SAMD3"    "IL18RAP" 
## [13] "PPP2R2B"  "L3MBTL4"  "SYTL2"   
## 
## $blue
##  [1] "ARHGAP15"   "PAG1"       "RBMS1"      "CDC14A"     "TMEM65"    
##  [6] "AKT3"       "INPP4B"     "ANK3"       "UST"        "PRKCA"     
## [11] "AL589693.1" "LEF1"       "KANK1"      "CMTM8"      "FMN1"      
## [16] "TIAM1"      "PTPN13"     "FAAH2"      "FRY"        "AC233976.1"
## [21] "SESN3"      "SAMD12"     "AC139720.1" "FHIT"       "RETREG1"   
## [26] "BCL2"       "ST8SIA1"    "GCNT4"      "CHN1"       "PHEX"      
## [31] "VPS54"      "AL353660.1" "BICDL1"     "FAM160A1"   "ADAM19"    
## [36] "CCR6"       "AFF3"       "FCHSD2"    
## 
## $green
##  [1] "DPYD"        "ANTXR2"      "GNAQ"        "SKAP1"       "PAM"        
##  [6] "TTN"         "IKZF2"       "LINC02694"   "CCDC141"     "AC093865.1" 
## [11] "STAM"        "CDHR3"       "AC013652.1"  "MIR181A1HG"  "TAFA2"      
## [16] "AL136456.1"  "PALM2-AKAP2" "ATXN7L1"     "F5"          "RTKN2"      
## [21] "ABLIM1"      "TOX"         "ENTPD1"      "LDLRAD4"     "TSHR"       
## [26] "ADAM12"      "TSHZ2"       "PLCL1"       "MCF2L2"      "ITGB1"      
## [31] "HPGD"        "MIR4435-2HG" "ARL15"       "MSC-AS1"     "DCP1B"      
## [36] "NIBAN1"      "JAZF1"       "ST8SIA6"     "KIAA1671"    "AHCYL2"     
## [41] "UBASH3B"     "CYP7B1"      "SGPP2"       "BCAS3"       "SH3RF3"     
## [46] "CD247"       "RBMS3"       "PLD1"       
## 
## [1] "5014_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.689
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50151
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 8.7471e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  RPLP2, RPL41, RPS19, IGKC, IL32, ARHGAP24, MALAT1, FOS, AC022217.3, JUN 
##     HDAC9, CD74, BANK1, FOSB, CD79A, MEF2C, WDFY4, IGHM, COL19A1, MS4A1 
## Negative:  ARHGAP15, SOS1, RORA, DPYD, RPS6KA3, PARP8, KAT2B, MBNL1, STAT4, PAG1 
##     CNOT6L, ATXN1, CDC14A, JMJD1C, THEMIS, RBMS1, BBS9, OSBPL3, TC2N, RABGAP1L 
## PC_ 2 
## Positive:  PRKCA, LEF1, SERINC5, TSHZ2, SESN3, PLCL1, MAML2, CMTM8, AL353660.1, MAP3K1 
##     AC139720.1, INPP4B, UBASH3B, CSGALNACT1, AC233976.1, MALAT1, GCNT4, FAAH2, RETREG1, TIAM1 
## Negative:  PLCB1, ZEB2, ARHGAP26, C1orf21, LINC00299, TGFBR3, SYTL2, GNLY, NCALD, AGAP1 
##     IL18RAP, PPP2R2B, LINC02384, AUTS2, MYBL1, SETBP1, AOAH, TMCC3, STAT4, GTDC1 
## PC_ 3 
## Positive:  PLXDC2, UGGT2, MEF2C, LRMDA, BACE2, LYN, DAPK1, DACH1, KHDRBS2, ADAM28 
##     AFF3, USP6NL, ARHGAP24, BANK1, CDK14, MYB, PDE3A, MED12L, MCTP1, CTDSPL 
## Negative:  ANK3, TC2N, RORA, MYBL1, THEMIS, STAT4, PARP8, RASGRF2, IL18RAP, IFNG-AS1 
##     EML4, PLCB1, TPRG1, SYTL2, PDE3B, DPP4, IL18R1, CD96, A2M, TGFBR3 
## PC_ 4 
## Positive:  ANK3, NELL2, BACH2, PCSK5, RASGRF2, PRKN, NR3C2, AC139720.1, INPP4B, FMN1 
##     ADAM23, RPLP2, MAN1C1, USP6NL, ZNF516, IGF1R, ZBTB20, IFNG-AS1, THEMIS, ARHGAP32 
## Negative:  IKZF2, AC093865.1, LINC02694, TOX, F5, AC013652.1, RTKN2, ST8SIA6, TTN, IL2RA 
##     STAM, CCDC141, PSD3, VAV3, NUSAP1, AL136456.1, MCF2L2, BRCA2, RBMS3, NIBAN1 
## PC_ 5 
## Positive:  BANK1, MS4A1, OSBPL10, TBC1D9, TCF4, ARHGAP24, MEF2C, KHDRBS2, IGKC, AFF3 
##     MARCH1, RALGPS2, CCSER1, WDFY4, COL19A1, CD74, PLEKHG1, IGHM, UBE2E2, FCRL5 
## Negative:  LSM2, AC078778.1, NKAIN2, SLC35G2, CACNB2, CDC42BPA, PBX1, ETS2, GOLIM4, AC055811.1 
##     MINPP1, RNF217, SLC40A1, AC010745.2, MEIS1, MYB, ITGA9-AS1, DPY19L2, PRKG2, ARHGEF28 
##    Power SFT.R.sq slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1   0.0378  7.25         0.8760 1.16e+02  1.15e+02 122.000
## 2      2   0.0212  2.52         0.7840 5.97e+01  5.93e+01  66.400
## 3      3   0.0109 -1.09         0.8360 3.12e+01  3.09e+01  37.100
## 4      4   0.1470 -2.86         0.8610 1.65e+01  1.62e+01  21.400
## 5      5   0.3050 -3.36         0.8270 8.84e+00  8.57e+00  12.700
## 6      6   0.5300 -3.75         0.8470 4.81e+00  4.59e+00   7.770
## 7      7   0.6850 -3.66         0.8290 2.66e+00  2.50e+00   4.910
## 8      8   0.8390 -3.28         0.8780 1.50e+00  1.37e+00   3.190
## 9      9   0.2820 -7.17         0.1360 8.61e-01  7.61e-01   2.130
## 10    10   0.8910 -2.72         0.8630 5.05e-01  4.31e-01   1.470
## 11    12   0.9410 -2.32         0.9250 1.86e-01  1.40e-01   0.797
## 12    14   0.9390 -1.99         0.9240 7.57e-02  4.64e-02   0.461
## 13    16   0.1580 -2.48        -0.0318 3.37e-02  1.64e-02   0.280
## 14    18   0.1660 -2.27        -0.0301 1.64e-02  6.13e-03   0.175
## 15    20   0.2090 -2.29        -0.0131 8.57e-03  2.35e-03   0.118

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4 
## 165  27  13  12  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
## $brown
##  [1] "IGKC"     "ARHGAP24" "CD74"     "BANK1"    "CD79A"    "MEF2C"   
##  [7] "IGHM"     "COL19A1"  "MS4A1"    "PLXDC2"   "AFF3"     "SWAP70"  
## 
## $yellow
##  [1] "RORA"      "PARP8"     "STAT4"     "THEMIS"    "PLCB1"     "LINC00299"
##  [7] "SYTL2"     "IL18RAP"   "MYBL1"     "MVB12B"   
## 
## $turquoise
##  [1] "LRMDA"      "DACH1"      "MYB"        "PDE3A"      "CTDSPL"    
##  [6] "SLC40A1"    "AC078778.1" "ICA1"       "LSM2"       "SLC35G2"   
## [11] "CACNB2"     "CDC42BPA"   "PBX1"       "ETS2"       "GOLIM4"    
## [16] "AC055811.1" "MINPP1"     "RNF217"     "AC010745.2" "MEIS1"     
## [21] "ITGA9-AS1"  "DPY19L2"    "ARHGEF28"   "MERTK"      "MGST2"     
## [26] "DEPTOR"     "AF233439.1"
## 
## $blue
##  [1] "ST5"        "KIF11"      "CIT"        "CENPM"      "CDCA8"     
##  [6] "KNL1"       "ESCO2"      "CDC25A"     "HIST1H2AL"  "FOXM1"     
## [11] "DTL"        "BX004807.1" "SOX2-OT"   
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $brown
##  [1] "IGKC"     "ARHGAP24" "CD74"     "BANK1"    "CD79A"    "MEF2C"   
##  [7] "IGHM"     "COL19A1"  "MS4A1"    "PLXDC2"   "AFF3"     "SWAP70"  
## 
## $yellow
##  [1] "RORA"      "PARP8"     "STAT4"     "THEMIS"    "PLCB1"     "LINC00299"
##  [7] "SYTL2"     "IL18RAP"   "MYBL1"     "MVB12B"   
## 
## $turquoise
##  [1] "LRMDA"      "DACH1"      "MYB"        "PDE3A"      "CTDSPL"    
##  [6] "SLC40A1"    "AC078778.1" "ICA1"       "LSM2"       "SLC35G2"   
## [11] "CACNB2"     "CDC42BPA"   "PBX1"       "ETS2"       "GOLIM4"    
## [16] "AC055811.1" "MINPP1"     "RNF217"     "AC010745.2" "MEIS1"     
## [21] "ITGA9-AS1"  "DPY19L2"    "ARHGEF28"   "MERTK"      "MGST2"     
## [26] "DEPTOR"     "AF233439.1"
## 
## $blue
##  [1] "ST5"        "KIF11"      "CIT"        "CENPM"      "CDCA8"     
##  [6] "KNL1"       "ESCO2"      "CDC25A"     "HIST1H2AL"  "FOXM1"     
## [11] "DTL"        "BX004807.1" "SOX2-OT"   
## 
## [1] "5023_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.8432
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50212
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 3.747e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  ARHGAP15, CDC14A, INPP4B, ANK3, MDFIC, THEMIS, MBNL1, RORA, DOCK10, PRKCA 
##     GPRIN3, SOS1, PARP8, PDE3B, LEF1, RBMS1, KLF12, RUNX2, DPYD, SKAP1 
## Negative:  RPL41, BANK1, RPL13A, RPS23, RPLP1, RPL28, RPS18, LYN, RPL13, RPLP2 
##     ZEB2, AFF3, RPS2, RPL3, EBF1, TMSB10, RPS19, VCAN, RPL12, RPL18A 
## PC_ 2 
## Positive:  ZEB2, AOAH, LYN, C1orf21, GTDC1, ARHGAP26, BANK1, SETBP1, DTHD1, PDGFD 
##     TGFBR3, MAP3K8, GAS7, VCAN, KLRK1, SAMD3, LINC02384, PPP2R2B, EBF1, NCALD 
## Negative:  PRKCA, LEF1, INPP4B, LTB, AC139720.1, TSHZ2, RPL13, TMSB10, RPL13A, CMTM8 
##     RPS18, RPS28, RPLP2, EEF1A1, RPL18, ANK3, RPL3, KANK1, TXK, FHIT 
## PC_ 3 
## Positive:  RPLP2, RPS19, RPS2, RPS28, RPL28, RPL18A, RPL13, EEF1A1, RPS23, LTB 
##     RPLP1, RPL12, RPL18, RPL3, RPS18, RPL41, AP001011.1, TMSB10, RPL13A, TRBC2 
## Negative:  ZSWIM5, PLCB1, PRKCA, BTBD11, MYO1D, SDK2, EFCAB8, TIAM1, IGF1R, ELOVL6 
##     CNNM2, PLXNA4, MAP2K6, SAMD12, EXPH5, TTLL11, EPHB1, ACYP2, ZFYVE9, TAFA1 
## PC_ 4 
## Positive:  LINC02694, TOX, TSHR, CDHR3, SLC9A9, TTN, IKZF2, CCDC141, AC013652.1, AC093865.1 
##     RTKN2, STAM, F5, IL7, ATXN7L1, CYTOR, TSHZ2, ZC2HC1A, LINC01362, FHIT 
## Negative:  PDE4D, PLCB1, BACH2, ADAM23, NELL2, RBMS1, MYBL1, SBF2, PZP, NRIP1 
##     PCSK5, EDA, A2M, NR3C2, UBE2E2, RPS2, CR1, ALOX5, SNTG2, CFH 
## PC_ 5 
## Positive:  BANK1, LYN, CERS6, EBF1, VCAN, DMXL2, AFF3, GRK3, CCSER1, PLXDC2 
##     IGKC, ZEB2, TRIO, MTSS1, APBA2, IGF1R, MAML3, NEXMIF, SETBP1, SESN3 
## Negative:  LINC00299, FRY, PLCB1, MSC-AS1, RORA, B4GALT5, AL136456.1, NTN4, LINC02694, SYTL2 
##     NCALD, MYBL1, RUNX2, IL18RAP, IL18R1, PTPN13, TRIQK, CASC8, PDE4D, DLEU1 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.   max.k.
## 1      1    0.666 -29.20          0.804 1.03e+02  1.03e+02 109.0000
## 2      2    0.572 -14.70          0.654 5.32e+01  5.28e+01  59.9000
## 3      3    0.512  -7.94          0.716 2.77e+01  2.73e+01  33.3000
## 4      4    0.514  -5.66          0.818 1.46e+01  1.42e+01  18.8000
## 5      5    0.489  -3.93          0.712 7.79e+00  7.49e+00  10.8000
## 6      6    0.489  -2.53          0.580 4.21e+00  3.96e+00   6.2900
## 7      7    0.499  -2.06          0.437 2.31e+00  2.13e+00   3.8600
## 8      8    0.867  -2.50          0.832 1.29e+00  1.16e+00   2.6000
## 9      9    0.902  -2.40          0.875 7.33e-01  6.23e-01   1.8000
## 10    10    0.956  -2.23          0.962 4.26e-01  3.42e-01   1.2800
## 11    12    0.894  -1.84          0.944 1.54e-01  1.04e-01   0.6850
## 12    14    0.786  -1.61          0.781 6.07e-02  3.25e-02   0.3800
## 13    16    0.878  -1.40          0.908 2.62e-02  1.05e-02   0.2160
## 14    18    0.811  -1.29          0.807 1.22e-02  3.41e-03   0.1240
## 15    20    0.896  -1.19          0.890 5.98e-03  1.17e-03   0.0717

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  0  1  2  3  4  5  6  7  8 
## 68 37 20 17 16 13 12 10 10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
## $turquoise
##  [1] "ARHGAP15"   "CDC14A"     "INPP4B"     "ANK3"       "MDFIC"     
##  [6] "THEMIS"     "MBNL1"      "DOCK10"     "PRKCA"      "GPRIN3"    
## [11] "PARP8"      "PDE3B"      "LEF1"       "KLF12"      "DPYD"      
## [16] "EPHA4"      "SUPT3H"     "MAML2"      "GNAQ"       "LPP"       
## [21] "AC139720.1" "TSHZ2"      "CMTM8"      "TXK"        "FHIT"      
## [26] "FAAH2"      "ACYP2"      "TAFA1"      "SLC9A9"     "LINC01362" 
## [31] "LINC01727"  "ST8SIA1"    "NELL2"      "NR3C2"      "RASGRF2"   
## [36] "PCAT1"      "PLCL1"     
## 
## $blue
##  [1] "RORA"      "SOS1"      "RBMS1"     "RUNX2"     "PLCB1"     "ZSWIM5"   
##  [7] "ELOVL6"    "CNNM2"     "PDE4D"     "MYBL1"     "CR1"       "SNTG2"    
## [13] "ABCB1"     "LINC00299" "FRY"       "B4GALT5"   "TRIQK"     "TNFAIP3"  
## [19] "DST"       "MTUS2"    
## 
## $black
##  [1] "BANK1"  "LYN"    "ZEB2"   "AFF3"   "EBF1"   "VCAN"   "IGKC"   "SETBP1"
##  [9] "AOAH"   "MAP3K8" "GRK3"   "PLXDC2" "SKAP2"  "UBE2E2" "ALOX5"  "DMXL2" 
## [17] "CCSER1" "TRIO"   "MAML3"  "TCF7L2"
## 
## $yellow
##  [1] "RPS23"  "RPLP1"  "RPL28"  "RPS18"  "RPL13"  "RPLP2"  "RPS2"   "RPL3"  
##  [9] "TMSB10" "RPS19"  "RPS28"  "EEF1A1" "RPL18"  "TRBC1"  "TRBC2"  "ID2"   
## 
## $green
##  [1] "C1orf21"   "GTDC1"     "DTHD1"     "PDGFD"     "TGFBR3"    "GAS7"     
##  [7] "KLRK1"     "SAMD3"     "LINC02384" "PPP2R2B"   "NCALD"     "SYTL2"    
## [13] "MCTP2"    
## 
## $brown
##  [1] "AC013652.1" "LINC02694"  "TOX"        "TSHR"       "CDHR3"     
##  [6] "TTN"        "IKZF2"      "CCDC141"    "AC093865.1" "RTKN2"     
## [11] "STAM"       "IL7"        "ATXN7L1"    "CYTOR"      "ZC2HC1A"   
## [16] "XYLB"       "EZH2"      
## 
## $red
##  [1] "F5"         "AL136456.1" "NTN4"       "PTPN13"     "DLEU1"     
##  [6] "CYTH3"      "AL589693.1" "COL5A3"     "NEDD4L"     "MCF2L2"    
## [11] "MAPK10"     "KLF7"      
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
##  [1] "ARHGAP15"   "CDC14A"     "INPP4B"     "ANK3"       "MDFIC"     
##  [6] "THEMIS"     "MBNL1"      "DOCK10"     "PRKCA"      "GPRIN3"    
## [11] "PARP8"      "PDE3B"      "LEF1"       "KLF12"      "DPYD"      
## [16] "EPHA4"      "SUPT3H"     "MAML2"      "GNAQ"       "LPP"       
## [21] "AC139720.1" "TSHZ2"      "CMTM8"      "TXK"        "FHIT"      
## [26] "FAAH2"      "ACYP2"      "TAFA1"      "SLC9A9"     "LINC01362" 
## [31] "LINC01727"  "ST8SIA1"    "NELL2"      "NR3C2"      "RASGRF2"   
## [36] "PCAT1"      "PLCL1"     
## 
## $blue
##  [1] "RORA"      "SOS1"      "RBMS1"     "RUNX2"     "PLCB1"     "ZSWIM5"   
##  [7] "ELOVL6"    "CNNM2"     "PDE4D"     "MYBL1"     "CR1"       "SNTG2"    
## [13] "ABCB1"     "LINC00299" "FRY"       "B4GALT5"   "TRIQK"     "TNFAIP3"  
## [19] "DST"       "MTUS2"    
## 
## $black
##  [1] "BANK1"  "LYN"    "ZEB2"   "AFF3"   "EBF1"   "VCAN"   "IGKC"   "SETBP1"
##  [9] "AOAH"   "MAP3K8" "GRK3"   "PLXDC2" "SKAP2"  "UBE2E2" "ALOX5"  "DMXL2" 
## [17] "CCSER1" "TRIO"   "MAML3"  "TCF7L2"
## 
## $yellow
##  [1] "RPS23"  "RPLP1"  "RPL28"  "RPS18"  "RPL13"  "RPLP2"  "RPS2"   "RPL3"  
##  [9] "TMSB10" "RPS19"  "RPS28"  "EEF1A1" "RPL18"  "TRBC1"  "TRBC2"  "ID2"   
## 
## $green
##  [1] "C1orf21"   "GTDC1"     "DTHD1"     "PDGFD"     "TGFBR3"    "GAS7"     
##  [7] "KLRK1"     "SAMD3"     "LINC02384" "PPP2R2B"   "NCALD"     "SYTL2"    
## [13] "MCTP2"    
## 
## $brown
##  [1] "AC013652.1" "LINC02694"  "TOX"        "TSHR"       "CDHR3"     
##  [6] "TTN"        "IKZF2"      "CCDC141"    "AC093865.1" "RTKN2"     
## [11] "STAM"       "IL7"        "ATXN7L1"    "CYTOR"      "ZC2HC1A"   
## [16] "XYLB"       "EZH2"      
## 
## $red
##  [1] "F5"         "AL136456.1" "NTN4"       "PTPN13"     "DLEU1"     
##  [6] "CYTH3"      "AL589693.1" "COL5A3"     "NEDD4L"     "MCF2L2"    
## [11] "MAPK10"     "KLF7"      
## 
## [1] "5014_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.7275
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.2652e-15

## PC_ 1 
## Positive:  PARP8, PLCB1, ARHGAP26, THEMIS, PDZD8, RORA, TGFBR3, ARHGAP15, MYBL1, NCALD 
##     LINC01619, PPP3CA, PAM, MVB12B, NIBAN1, SIK3, LINC00299, IFNG-AS1, AF165147.1, ZEB2 
## Negative:  RPL13, RPL28, RPLP2, RPL41, RPS18, EEF1A1, TPT1, RPS8, RPS19, RPLP1 
##     RPL38, RPS2, RPS23, RPL11, RPS28, RPS12, RPL18A, RPL12, RPL36A, RPS15 
## PC_ 2 
## Positive:  PRKCA, SERINC5, INPP4B, LEF1, TXK, GNAQ, AC139720.1, CAMK4, SESN3, MGAT5 
##     LDLRAD4, TSHZ2, CMTM8, ARHGAP15, PELI1, MAML2, PAG1, TIAM1, FAAH2, CSGALNACT1 
## Negative:  ZEB2, ARHGAP26, C1orf21, GNLY, AOAH, SETBP1, AGAP1, LINC02384, PDGFD, TGFBR3 
##     SYTL2, PPP2R2B, KLRD1, MVB12B, NKG7, A2M, AL392086.3, DTHD1, NCALD, EIF4G3 
## PC_ 3 
## Positive:  TOX, IKZF2, AC093865.1, CCDC141, TTN, STAM, RTKN2, ST8SIA6, MIR181A1HG, HPGD 
##     VAV3, CDHR3, F5, MAP3K1, LINC02694, AC090125.1, ZEB2, ATP8A1, AC243829.2, FCRL3 
## Negative:  ANK3, PLCB1, IFNG-AS1, RBMS1, NR3C2, NELL2, PELI2, BCL2, MYBL1, CASC8 
##     RPLP2, CDC14A, A2M, TNFAIP3, PZP, ME1, RPS19, SBF2, EEF1A1, RPL13 
## PC_ 4 
## Positive:  IFNG-AS1, UBASH3B, SERINC5, FAAH2, BTBD11, AC245060.5, ETV6, DIRC3, AL078604.4, ROR2 
##     PAG1, LRRC8D, CENPF, DHRSX, MKI67, FAM184A, ZBTB16, ABCB9, SLC5A11, ANK3 
## Negative:  RPL11, EEF1A1, RPLP2, RPS12, RPS15, RPL18A, RPS2, RPS19, RPL28, RPL13 
##     RPS8, RPL38, RPL41, RPS23, RPS18, RPS28, TPT1, RPL36A, RPL12, RPLP1 
## PC_ 5 
## Positive:  KLRK1, IGF1R, TXK, AOAH, AC243829.2, AL353660.1, GFOD1, PIK3AP1, MTSS1, C1orf21 
##     BNC2, KLRD1, LYN, DENND5A, GNLY, EPHA1-AS1, PRKCA, BANK1, CMTM8, RALGPS2 
## Negative:  LINC02694, AC013652.1, HPGD, NIBAN1, AL136456.1, IL12RB2, RORA, MSC-AS1, CCR6, ZC2HC1A 
##     ADAM12, RBPJ, DLEU2, STAM, TNFAIP3, B4GALT5, CCDC141, PHACTR2, PAG1, NEDD4L 
##    Power SFT.R.sq     slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1 3.28e-01 -51.40000         0.8680 114.0000  1.14e+02 117.000
## 2      2 1.40e-01 -11.90000         0.8450  58.1000  5.81e+01  61.400
## 3      3 2.28e-01  -7.75000         0.3280  29.9000  2.98e+01  33.400
## 4      4 5.77e-01  -8.14000         0.4570  15.6000  1.54e+01  19.600
## 5      5 4.94e-01  -5.86000         0.4880   8.2400  8.00e+00  12.300
## 6      6 4.45e-01  -4.18000         0.6190   4.4300  4.20e+00   8.200
## 7      7 4.39e-01  -3.15000         0.7240   2.4400  2.22e+00   5.770
## 8      8 3.96e-02  -2.44000         0.1020   1.3700  1.18e+00   4.250
## 9      9 1.22e-02  -1.46000         0.2130   0.7980  6.37e-01   3.230
## 10    10 1.84e-02  -1.13000         0.0816   0.4800  3.43e-01   2.520
## 11    12 5.32e-05  -0.06230         0.2180   0.1950  1.03e-01   1.590
## 12    14 1.86e-02   0.96900         0.1890   0.0912  3.21e-02   1.040
## 13    16 4.50e-06   0.00976         0.0175   0.0480  1.01e-02   0.685
## 14    18 3.28e-03  -0.23100         0.0281   0.0274  3.32e-03   0.456
## 15    20 9.28e-03  -0.35000        -0.0184   0.0163  1.07e-03   0.305

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  1  2  3  4  5  6  7  8  9 10 
## 49 25 23 23 22 21 20 18 14 12

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 10 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.
## $brown
##  [1] "PARP8"      "PLCB1"      "ARHGAP26"   "THEMIS"     "PDZD8"     
##  [6] "RORA"       "MYBL1"      "PPP3CA"     "PAM"        "NIBAN1"    
## [11] "SIK3"       "LINC00299"  "IFNG-AS1"   "AF165147.1" "SFMBT2"    
## [16] "IL18RAP"    "GTDC1"      "SBF2"       "TANC2"      "B4GALT5"   
## [21] "SLC4A10"    "COLQ"       "TPRG1"     
## 
## $turquoise
##  [1] "TGFBR3"     "NCALD"      "LINC01619"  "MVB12B"     "ZEB2"      
##  [6] "SYTL2"      "PPP2R2B"    "C1orf21"    "GNLY"       "AOAH"      
## [11] "SETBP1"     "AGAP1"      "LINC02384"  "PDGFD"      "KLRD1"     
## [16] "NKG7"       "A2M"        "AL392086.3" "DTHD1"      "EIF4G3"    
## [21] "AC243829.2" "KLRF1"      "YES1"       "CEP78"      "ST8SIA6"   
## [26] "ATP8A1"     "KLRK1"      "TNFAIP3"    "PZP"        "CFH"       
## [31] "BTBD11"     "HIP1"       "MBNL1"      "GFOD1"      "PIK3AP1"   
## [36] "MTSS1"      "BNC2"       "LYN"        "SGCD"       "PPM1L"     
## [41] "KLRC4"      "DLEU2"      "PHACTR2"    "ATF7IP2"    "LRIG1"     
## [46] "NEAT1"      "TAFA1"      "KIAA0825"   "ERI1"      
## 
## $blue
##  [1] "ARHGAP15"   "PRKCA"      "SERINC5"    "INPP4B"     "CAMK4"     
##  [6] "MGAT5"      "LDLRAD4"    "PELI1"      "MAML2"      "PAG1"      
## [11] "FAAH2"      "MYO16"      "SSBP2"      "CDC14A"     "FMN1"      
## [16] "ANK3"       "RBMS1"      "NR3C2"      "NELL2"      "BCL2"      
## [21] "UBASH3B"    "ETV6"       "DIRC3"      "AL078604.4" "LRRC8D"    
## [26] "ZBTB16"     "SLC5A11"    "AC104170.1" "BACH2"      "AL136456.1"
## [31] "CCR6"       "ADAM12"     "MCF2L2"     "GCNT4"      "ST8SIA1"   
## [36] "FRY"        "ADAM19"     "PTPN13"     "RUNX2"      "ELOVL4"    
## [41] "SAMD12"     "SNX9"       "RNF19A"    
## 
## $yellow
##  [1] "RPL13"  "RPL28"  "RPLP2"  "RPL41"  "RPS18"  "EEF1A1" "TPT1"   "RPS8"  
##  [9] "RPS19"  "RPLP1"  "RPL38"  "RPS2"   "RPS23"  "RPL11"  "RPS28"  "RPS12" 
## [17] "RPL18A" "RPL12"  "RPL36A" "RPS15"  "JUN"    "JUNB"   "PLCG2" 
## 
## $magenta
##  [1] "TSHZ2"      "AL109930.1" "LEF1"       "TXK"        "AC139720.1"
##  [6] "SESN3"      "CMTM8"      "PHEX"       "IGF1R"      "AL353660.1"
## [11] "DENND5A"    "EPHA1-AS1"  "AL589693.1" "SLC22A23"  
## 
## $red
##  [1] "PLCL1"      "TOX"        "IKZF2"      "AC093865.1" "CCDC141"   
##  [6] "TTN"        "STAM"       "RTKN2"      "VAV3"       "F5"        
## [11] "AC090125.1" "FCRL3"      "AC245060.5" "CENPF"      "MKI67"     
## [16] "FAM184A"    "TAFA2"      "RBMS3"      "CDK14"      "SGPP2"     
## [21] "AP002383.2"
## 
## $purple
##  [1] "GNAQ"       "TIAM1"      "CSGALNACT1" "MAP3K1"     "SNED1"     
##  [6] "DHRSX"      "USP46"      "PKIA"       "LINC01362"  "SEMA5A"    
## [11] "EGLN3"      "LINC00511" 
## 
## $black
##  [1] "MIR181A1HG" "HPGD"       "CDHR3"      "LINC02694"  "ROR2"      
##  [6] "ABCB9"      "BANK1"      "RALGPS2"    "LARGE1"     "AC013652.1"
## [11] "MSC-AS1"    "ZC2HC1A"    "NEDD4L"     "MAF"        "AFF3"      
## [16] "WDFY4"      "OSBPL10"    "IGKC"       "ARHGAP24"   "BLK"       
## 
## $green
##  [1] "MIR4435-2HG" "PELI2"       "CASC8"       "ME1"         "SLC16A1-AS1"
##  [6] "IL12RB2"     "RBPJ"        "RGS1"        "CENPE"       "TBXAS1"     
## [11] "TLE1"        "PTPRM"       "TANC1"       "LINC01146"   "ATP1B1"     
## [16] "MIR31HG"     "LINC00944"   "ZNF365"      "ADAM22"      "ANXA1"      
## [21] "AC011997.1"  "PACSIN1"    
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "638/10000 permutations failed the Mann-Whitney test."
## [1] "1159/10000 permutations failed the Mann-Whitney test."
## [1] "6471/10000 permutations failed the Mann-Whitney test."
## $brown
##  [1] "PARP8"      "PLCB1"      "ARHGAP26"   "THEMIS"     "PDZD8"     
##  [6] "RORA"       "MYBL1"      "PPP3CA"     "PAM"        "NIBAN1"    
## [11] "SIK3"       "LINC00299"  "IFNG-AS1"   "AF165147.1" "SFMBT2"    
## [16] "IL18RAP"    "GTDC1"      "SBF2"       "TANC2"      "B4GALT5"   
## [21] "SLC4A10"    "COLQ"       "TPRG1"     
## 
## $turquoise
##  [1] "TGFBR3"     "NCALD"      "LINC01619"  "MVB12B"     "ZEB2"      
##  [6] "SYTL2"      "PPP2R2B"    "C1orf21"    "GNLY"       "AOAH"      
## [11] "SETBP1"     "AGAP1"      "LINC02384"  "PDGFD"      "KLRD1"     
## [16] "NKG7"       "A2M"        "AL392086.3" "DTHD1"      "EIF4G3"    
## [21] "AC243829.2" "KLRF1"      "YES1"       "CEP78"      "ST8SIA6"   
## [26] "ATP8A1"     "KLRK1"      "TNFAIP3"    "PZP"        "CFH"       
## [31] "BTBD11"     "HIP1"       "MBNL1"      "GFOD1"      "PIK3AP1"   
## [36] "MTSS1"      "BNC2"       "LYN"        "SGCD"       "PPM1L"     
## [41] "KLRC4"      "DLEU2"      "PHACTR2"    "ATF7IP2"    "LRIG1"     
## [46] "NEAT1"      "TAFA1"      "KIAA0825"   "ERI1"      
## 
## $blue
##  [1] "ARHGAP15"   "PRKCA"      "SERINC5"    "INPP4B"     "CAMK4"     
##  [6] "MGAT5"      "LDLRAD4"    "PELI1"      "MAML2"      "PAG1"      
## [11] "FAAH2"      "MYO16"      "SSBP2"      "CDC14A"     "FMN1"      
## [16] "ANK3"       "RBMS1"      "NR3C2"      "NELL2"      "BCL2"      
## [21] "UBASH3B"    "ETV6"       "DIRC3"      "AL078604.4" "LRRC8D"    
## [26] "ZBTB16"     "SLC5A11"    "AC104170.1" "BACH2"      "AL136456.1"
## [31] "CCR6"       "ADAM12"     "MCF2L2"     "GCNT4"      "ST8SIA1"   
## [36] "FRY"        "ADAM19"     "PTPN13"     "RUNX2"      "ELOVL4"    
## [41] "SAMD12"     "SNX9"       "RNF19A"    
## 
## $yellow
##  [1] "RPL13"  "RPL28"  "RPLP2"  "RPL41"  "RPS18"  "EEF1A1" "TPT1"   "RPS8"  
##  [9] "RPS19"  "RPLP1"  "RPL38"  "RPS2"   "RPS23"  "RPL11"  "RPS28"  "RPS12" 
## [17] "RPL18A" "RPL12"  "RPL36A" "RPS15"  "JUN"    "JUNB"   "PLCG2" 
## 
## $magenta
##  [1] "TSHZ2"      "AL109930.1" "LEF1"       "TXK"        "AC139720.1"
##  [6] "SESN3"      "CMTM8"      "PHEX"       "IGF1R"      "AL353660.1"
## [11] "DENND5A"    "EPHA1-AS1"  "AL589693.1" "SLC22A23"  
## 
## $red
##  [1] "PLCL1"      "TOX"        "IKZF2"      "AC093865.1" "CCDC141"   
##  [6] "TTN"        "STAM"       "RTKN2"      "VAV3"       "F5"        
## [11] "AC090125.1" "FCRL3"      "AC245060.5" "CENPF"      "MKI67"     
## [16] "FAM184A"    "TAFA2"      "RBMS3"      "CDK14"      "SGPP2"     
## [21] "AP002383.2"
## 
## [1] "5017_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.4134
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49961
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 9.8439e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  ARHGAP15, THEMIS, ANK3, INPP4B, ANKRD44, ADAM19, SERINC5, PATJ, PAG1, SIK3 
##     RIPOR2, RORA, FMN1, FOXP1, SOS1, XKR6, PDE7A, AKT3, KLF12, MYBL1 
## Negative:  B2M, RPLP2, RPL13, RPS19, HLA-A, RPS27, IL32, TMSB10, ACTG1, CD52 
##     LTB, TPT1, S100A4, IKZF2, JUN, JUNB, TRAC, CD74, FOS, TRBC1 
## PC_ 2 
## Positive:  NKG7, KLRD1, CCL5, ZEB2, GNLY, KLRK1, KLRC2, PPP2R2B, AC243829.2, EPB41L4A 
##     PRF1, GZMH, SGCD, TGFBR3, DTHD1, GZMB, GZMA, ARHGAP26, PLEK, AOAH 
## Negative:  LEF1, FHIT, LTB, SERINC5, ANK3, PRKCA, FAM13A, TSHZ2, MAP3K1, SESN3 
##     CMTM8, TPT1, PCSK5, MAML2, ALPK1, TRABD2A, FAAH2, NELL2, RPL13, MLLT3 
## PC_ 3 
## Positive:  ANK3, AOAH, SNTB1, ZEB2, NKG7, THEMIS, CCL5, SETBP1, GNLY, NELL2 
##     APBA2, PLCB1, KLRD1, NR3C2, GZMH, IFNG-AS1, A2M, EPB41L4A, MCOLN2, AC243829.2 
## Negative:  LINC02694, STAM, AC013652.1, IKZF2, CCDC141, IL2RA, ITGB1, AC093865.1, AL136456.1, MIR181A1HG 
##     NIBAN1, TTN, ZC3H12C, CASK, RTKN2, SGMS1, CDK14, DUSP4, TSHR, S100A4 
## PC_ 4 
## Positive:  MKI67, KIAA0825, KIF11, AHNAK, CHST11, CENPF, ASPM, AC105402.3, SLC16A10, LINC02725 
##     CIP2A, POC1A, CENPE, INCENP, ZSWIM5, TOP2A, CEP128, CDCA2, APOLD1, RGL1 
## Negative:  B2M, HLA-A, RPL13, LTB, FOSB, RPS19, RPLP2, RPS27, TPT1, JUNB 
##     PCSK5, JUN, PLCG2, IL32, MBNL1, TXK, PLXNA4, ACTG1, FAM13A, TMSB10 
## PC_ 5 
## Positive:  ZNF365, SEMA5A, RUNX2, PRKX, TGFBR3, ADAM19, FRY, GATA3, PPARG, LINC02694 
##     INPP4B, VEZT, CSGALNACT1, SCCPDH, KIAA0825, FOSB, AC013652.1, JUN, LGALS3, EGLN3 
## Negative:  TXK, VAV3, SMG9, LINC01727, CDK14, PLCL1, FRS2, TRPS1, LARGE1, DIAPH3 
##     CD79A, RBM7, RALGPS2, KIF13A, ITGA4, ZSWIM6, ARHGAP24, SLC8A1, SYK, CD86 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1    0.490 -39.40         0.9330 128.0000  1.27e+02 134.000
## 2      2    0.439 -16.20         0.9340  65.6000  6.56e+01  72.500
## 3      3    0.412  -9.11         0.8100  34.3000  3.41e+01  40.000
## 4      4    0.520  -6.62         0.8570  18.2000  1.80e+01  23.200
## 5      5    0.681  -5.82         0.9180   9.7900  9.62e+00  14.000
## 6      6    0.804  -5.19         0.9590   5.3800  5.17e+00   8.910
## 7      7    0.889  -4.18         0.9590   3.0200  2.81e+00   5.910
## 8      8    0.926  -3.43         0.9600   1.7400  1.55e+00   4.090
## 9      9    0.813  -3.00         0.7620   1.0300  8.71e-01   2.930
## 10    10    0.879  -2.48         0.8480   0.6300  4.92e-01   2.180
## 11    12    0.952  -2.04         0.9400   0.2590  1.65e-01   1.520
## 12    14    0.263  -3.11         0.0630   0.1220  5.98e-02   1.240
## 13    16    0.236  -2.49         0.0183   0.0658  2.22e-02   1.080
## 14    18    0.217  -3.12         0.0179   0.0395  8.59e-03   0.955
## 15    20    0.234  -2.95         0.0309   0.0260  3.46e-03   0.861

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5   6   7 
## 123  28  26  22  21  12  10  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
## $green
##  [1] "ARHGAP15" "THEMIS"   "ADAM19"   "PATJ"     "FMN1"     "SOS1"    
##  [7] "AKT3"     "MYBL1"    "CATSPERB" "CRYBG1"   "KIAA0825" "PRKX"    
## 
## $black
##  [1] "ANKRD44"  "SIK3"     "RORA"     "SLC9A9"   "MCOLN2"   "RABGAP1L"
##  [7] "XYLT1"    "SKAP1"    "AOPEP"    "SYNE1"   
## 
## $red
##  [1] "PAG1"    "RIPOR2"  "FOXP1"   "PDE7A"   "MAML2"   "FAAH2"   "MLLT3"  
##  [8] "RETREG1" "MBNL1"   "ZBTB20" 
## 
## $brown
##  [1] "B2M"        "RPLP2"      "RPL13"      "RPS19"      "HLA-A"     
##  [6] "RPS27"      "IL32"       "TMSB10"     "ACTG1"      "CD52"      
## [11] "LTB"        "TPT1"       "S100A4"     "JUN"        "JUNB"      
## [16] "TRAC"       "FOS"        "TRBC1"      "AC022217.3" "DUSP1"     
## [21] "FOSB"       "LINC00910" 
## 
## $yellow
##  [1] "CD74"       "HLA-DRB1"   "LRMDA"      "AC105402.3" "SMG9"      
##  [6] "LARGE1"     "CD79A"      "RBM7"       "RALGPS2"    "KIF13A"    
## [11] "SLC8A1"     "SYK"        "CD86"       "UBE2E2"     "CYBB"      
## [16] "PRKY"       "UTY"        "DDX3Y"      "AC114763.1" "HLA-DQB1"  
## [21] "LINC00278" 
## 
## $blue
##  [1] "NKG7"       "KLRD1"      "CCL5"       "ZEB2"       "GNLY"      
##  [6] "KLRK1"      "KLRC2"      "PPP2R2B"    "AC243829.2" "EPB41L4A"  
## [11] "PRF1"       "GZMH"       "SGCD"       "TGFBR3"     "DTHD1"     
## [16] "GZMB"       "GZMA"       "ARHGAP26"   "PLEK"       "AOAH"      
## [21] "PTGDR"      "KLRC3"      "IFNG"       "A2M"        "AC026470.2"
## [26] "KLRC4"     
## 
## $turquoise
##  [1] "MKI67"      "KIF11"      "CENPF"      "ASPM"       "LINC02725" 
##  [6] "CIP2A"      "POC1A"      "CENPE"      "INCENP"     "CDCA2"     
## [11] "RGL1"       "MELK"       "DIAPH3"     "AC104850.2" "NEIL3"     
## [16] "SGO2"       "KNL1"       "E2F2"       "POLQ"       "FBXO43"    
## [21] "PHGDH"      "BUB1B"      "DTL"        "PDZD2"      "LIN9"      
## [26] "CCNB2"      "CEP152"     "TMEM44"    
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "49/10000 permutations failed the Mann-Whitney test."
## [1] "590/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $green
##  [1] "ARHGAP15" "THEMIS"   "ADAM19"   "PATJ"     "FMN1"     "SOS1"    
##  [7] "AKT3"     "MYBL1"    "CATSPERB" "CRYBG1"   "KIAA0825" "PRKX"    
## 
## $black
##  [1] "ANKRD44"  "SIK3"     "RORA"     "SLC9A9"   "MCOLN2"   "RABGAP1L"
##  [7] "XYLT1"    "SKAP1"    "AOPEP"    "SYNE1"   
## 
## $brown
##  [1] "B2M"        "RPLP2"      "RPL13"      "RPS19"      "HLA-A"     
##  [6] "RPS27"      "IL32"       "TMSB10"     "ACTG1"      "CD52"      
## [11] "LTB"        "TPT1"       "S100A4"     "JUN"        "JUNB"      
## [16] "TRAC"       "FOS"        "TRBC1"      "AC022217.3" "DUSP1"     
## [21] "FOSB"       "LINC00910" 
## 
## $yellow
##  [1] "CD74"       "HLA-DRB1"   "LRMDA"      "AC105402.3" "SMG9"      
##  [6] "LARGE1"     "CD79A"      "RBM7"       "RALGPS2"    "KIF13A"    
## [11] "SLC8A1"     "SYK"        "CD86"       "UBE2E2"     "CYBB"      
## [16] "PRKY"       "UTY"        "DDX3Y"      "AC114763.1" "HLA-DQB1"  
## [21] "LINC00278" 
## 
## $blue
##  [1] "NKG7"       "KLRD1"      "CCL5"       "ZEB2"       "GNLY"      
##  [6] "KLRK1"      "KLRC2"      "PPP2R2B"    "AC243829.2" "EPB41L4A"  
## [11] "PRF1"       "GZMH"       "SGCD"       "TGFBR3"     "DTHD1"     
## [16] "GZMB"       "GZMA"       "ARHGAP26"   "PLEK"       "AOAH"      
## [21] "PTGDR"      "KLRC3"      "IFNG"       "A2M"        "AC026470.2"
## [26] "KLRC4"     
## 
## $turquoise
##  [1] "MKI67"      "KIF11"      "CENPF"      "ASPM"       "LINC02725" 
##  [6] "CIP2A"      "POC1A"      "CENPE"      "INCENP"     "CDCA2"     
## [11] "RGL1"       "MELK"       "DIAPH3"     "AC104850.2" "NEIL3"     
## [16] "SGO2"       "KNL1"       "E2F2"       "POLQ"       "FBXO43"    
## [21] "PHGDH"      "BUB1B"      "DTL"        "PDZD2"      "LIN9"      
## [26] "CCNB2"      "CEP152"     "TMEM44"    
## 
## [1] "5017_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.6196
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 3.7337e-16

## PC_ 1 
## Positive:  RPL41, RPS19, B2M, JUN, TRBC1, FOS, FOSB, AC103591.3, TTN, CLNK 
##     AP000787.1, AFF3, PPP1R15A, CROCC, SLC16A10, IER2, NEBL, TEX14, CCDC141, IKZF2 
## Negative:  ARHGAP15, LINC01619, PARP8, FYN, STAT4, INPP4B, PPP3CA, ZBTB20, RPS6KA3, SIK3 
##     ADAM19, ANK3, PAG1, SOS1, MBNL1, TC2N, CDC14A, THEMIS, RORA, PDE4B 
## PC_ 2 
## Positive:  ANK3, TC2N, NELL2, INPP4B, FMN1, FKBP5, IFNG-AS1, TGFBR2, APBA2, PRKCA 
##     PITPNC1, ADAM19, ITGA4, BTBD11, THEMIS, BACH2, RASGRF2, MCOLN2, A2M, PELI2 
## Negative:  IKZF2, AC093865.1, LINC02694, AL136456.1, STAM, HPGD, IL2RA, TOX, ENTPD1, CCDC141 
##     TTN, MIR181A1HG, CDHR3, AC013652.1, CASK, RTKN2, VAV3, ZC2HC1A, NIBAN1, AC011997.1 
## PC_ 3 
## Positive:  AOAH, ZEB2, ARHGAP26, IL18RAP, C1orf21, DTHD1, SYTL3, MVB12B, PPP2R2B, IFNG-AS1 
##     GNLY, SAMD3, CCL5, PLCB1, TGFBR3, AGAP1, SYTL2, GZMH, CHST11, AF165147.1 
## Negative:  FHIT, SESN3, FAM13A, PRKCA, TSHZ2, AP000787.1, PLCL1, PLCG2, B2M, IMMP2L 
##     AFF3, AL109930.1, TAFA2, MBNL1, SPON1, PLXNA4, RETREG1, CMTM8, ZBTB20, BCL2 
## PC_ 4 
## Positive:  ATP8B4, ADAM28, C1orf21, TCF4, HDAC9, PLCB1, TRIO, MAML3, AUTS2, ANGPT1 
##     ZRANB2-AS2, PIP5K1B, SPOCK3, PRKG1, MED12L, PHACTR1, FLT1, MAGI2, ZEB2, VWDE 
## Negative:  CENPF, SGO2, KIF15, NCAPG, RRM2, KIF14, KIF18B, CDCA2, DLGAP5, PRR11 
##     MKI67, ASPM, BUB1, CENPE, BUB1B, POLQ, KIF18A, CCNB2, CDK1, CIT 
## PC_ 5 
## Positive:  SNED1, LINC02694, AC013652.1, NIBAN1, CSGALNACT1, ADAM19, SEMA5A, SYTL3, PAG1, GAB2 
##     CDHR3, CAMK4, PPP1R16B, IL2RA, KAT2B, RUNX2, ERN1, TGFBR3, TIAM1, AC005237.1 
## Negative:  KIF15, RRM2, CENPF, DLGAP5, GPC5, KIF18B, KIF14, CDCA2, SGO2, PRR11 
##     ASPM, NRIP1, CD38, KLHL13, NUSAP1, NCAPG, KIF18A, ATP8B4, PIP5K1B, CASC15 
##    Power SFT.R.sq slope truncated.R.sq  mean.k. median.k. max.k.
## 1      1   0.0655 12.30         0.9170 130.0000  1.30e+02 135.00
## 2      2   0.0034  1.12         0.9020  67.1000  6.70e+01  72.60
## 3      3   0.3010 -7.40         0.7100  34.8000  3.47e+01  40.90
## 4      4   0.5480 -7.96         0.6180  18.2000  1.80e+01  24.30
## 5      5   0.6500 -6.48         0.5610   9.6500  9.46e+00  15.50
## 6      6   0.7390 -5.40         0.6810   5.1800  5.00e+00  10.60
## 7      7   0.2750 -9.72         0.0879   2.8300  2.67e+00   7.74
## 8      8   0.2890 -7.77         0.1070   1.5800  1.44e+00   6.02
## 9      9   0.2290 -5.66         0.0393   0.9050  7.89e-01   4.91
## 10    10   0.1180 -2.58         0.1060   0.5360  4.32e-01   4.16
## 11    12   0.1450 -2.83        -0.0079   0.2130  1.34e-01   3.21
## 12    14   0.1470 -2.62        -0.0213   0.1030  4.29e-02   2.63
## 13    16   0.1640 -2.42        -0.0249   0.0610  1.40e-02   2.23
## 14    18   0.2560 -2.65         0.0437   0.0418  4.59e-03   1.94
## 15    20   0.1570 -2.10        -0.0302   0.0315  1.55e-03   1.71

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5   6   7   8 
## 131  27  26  16  14  11  11  10  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 7 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 7 module eigengenes in given set.
## $red
##  [1] "LINC01619" "PPP3CA"    "PAG1"      "NIBAN1"    "SYTL3"     "SAMD3"    
##  [7] "SYTL2"     "CHST11"    "TPRG1"     "PPP1R16B"  "KAT2B"    
## 
## $green
##  [1] "PARP8"      "FYN"        "STAT4"      "INPP4B"     "ZBTB20"    
##  [6] "SIK3"       "ANK3"       "MBNL1"      "TC2N"       "THEMIS"    
## [11] "PDE4B"      "ATP8A1"     "CBLB"       "TGFBR3"     "NELL2"     
## [16] "FKBP5"      "IFNG-AS1"   "TGFBR2"     "APBA2"      "PITPNC1"   
## [21] "BTBD11"     "BACH2"      "RASGRF2"    "MCOLN2"     "A2M"       
## [26] "PZP"        "DPP4"       "CYTH1"      "SBF2"       "BCL2"      
## [31] "AC139720.1" "CNOT6L"     "PCSK5"      "MYBL1"      "SLC9A9"    
## 
## $black
##  [1] "LINC02694"  "HPGD"       "CDHR3"      "AC013652.1" "AC011997.1"
##  [6] "ST8SIA6"    "GLCCI1"     "CD247"      "IPCEF1"     "LDLRAD4"   
## 
## $brown
##  [1] "AOAH"     "ZEB2"     "ARHGAP26" "IL18RAP"  "C1orf21"  "DTHD1"   
##  [7] "MVB12B"   "PPP2R2B"  "GNLY"     "CCL5"     "PLCB1"    "GZMH"    
## [13] "KLRD1"    "SLC4A4"   "EPB41L4A" "MCTP2"   
## 
## $turquoise
##  [1] "ATP8B4"     "ADAM28"     "TCF4"       "MAML3"      "ANGPT1"    
##  [6] "ZRANB2-AS2" "PIP5K1B"    "SPOCK3"     "PRKG1"      "MED12L"    
## [11] "PHACTR1"    "FLT1"       "MAGI2"      "VWDE"       "THRB"      
## [16] "AC092164.1" "LINC01122"  "B4GALT6"    "NKAIN2"     "GPC5"      
## [21] "NRIP1"      "KLHL13"     "CASC15"     "PPM1F"      "AL355612.1"
## [26] "CYSLTR2"    "DOCK5"     
## 
## $blue
##  [1] "CENPF"  "SGO2"   "KIF15"  "NCAPG"  "RRM2"   "KIF14"  "KIF18B" "CDCA2" 
##  [9] "DLGAP5" "PRR11"  "MKI67"  "ASPM"   "BUB1"   "CENPE"  "BUB1B"  "POLQ"  
## [17] "KIF18A" "CCNB2"  "CDK1"   "CIT"    "DIAPH3" "KNL1"   "TOP2A"  "CDCA8" 
## [25] "SGO1"   "NUSAP1"
## 
## [1] "69/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $red
##  [1] "LINC01619" "PPP3CA"    "PAG1"      "NIBAN1"    "SYTL3"     "SAMD3"    
##  [7] "SYTL2"     "CHST11"    "TPRG1"     "PPP1R16B"  "KAT2B"    
## 
## $green
##  [1] "PARP8"      "FYN"        "STAT4"      "INPP4B"     "ZBTB20"    
##  [6] "SIK3"       "ANK3"       "MBNL1"      "TC2N"       "THEMIS"    
## [11] "PDE4B"      "ATP8A1"     "CBLB"       "TGFBR3"     "NELL2"     
## [16] "FKBP5"      "IFNG-AS1"   "TGFBR2"     "APBA2"      "PITPNC1"   
## [21] "BTBD11"     "BACH2"      "RASGRF2"    "MCOLN2"     "A2M"       
## [26] "PZP"        "DPP4"       "CYTH1"      "SBF2"       "BCL2"      
## [31] "AC139720.1" "CNOT6L"     "PCSK5"      "MYBL1"      "SLC9A9"    
## 
## $black
##  [1] "LINC02694"  "HPGD"       "CDHR3"      "AC013652.1" "AC011997.1"
##  [6] "ST8SIA6"    "GLCCI1"     "CD247"      "IPCEF1"     "LDLRAD4"   
## 
## $brown
##  [1] "AOAH"     "ZEB2"     "ARHGAP26" "IL18RAP"  "C1orf21"  "DTHD1"   
##  [7] "MVB12B"   "PPP2R2B"  "GNLY"     "CCL5"     "PLCB1"    "GZMH"    
## [13] "KLRD1"    "SLC4A4"   "EPB41L4A" "MCTP2"   
## 
## $turquoise
##  [1] "ATP8B4"     "ADAM28"     "TCF4"       "MAML3"      "ANGPT1"    
##  [6] "ZRANB2-AS2" "PIP5K1B"    "SPOCK3"     "PRKG1"      "MED12L"    
## [11] "PHACTR1"    "FLT1"       "MAGI2"      "VWDE"       "THRB"      
## [16] "AC092164.1" "LINC01122"  "B4GALT6"    "NKAIN2"     "GPC5"      
## [21] "NRIP1"      "KLHL13"     "CASC15"     "PPM1F"      "AL355612.1"
## [26] "CYSLTR2"    "DOCK5"     
## 
## $blue
##  [1] "CENPF"  "SGO2"   "KIF15"  "NCAPG"  "RRM2"   "KIF14"  "KIF18B" "CDCA2" 
##  [9] "DLGAP5" "PRR11"  "MKI67"  "ASPM"   "BUB1"   "CENPE"  "BUB1B"  "POLQ"  
## [17] "KIF18A" "CCNB2"  "CDK1"   "CIT"    "DIAPH3" "KNL1"   "TOP2A"  "CDCA8" 
## [25] "SGO1"   "NUSAP1"
## 
## [1] "5023_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.5512
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50073
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 3.8809e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  ARHGAP15, MBNL1, DPYD, DOCK10, PAG1, CDC14A, MDFIC, CD96, RBMS1, GPRIN3 
##     INPP4B, RORA, STAT4, ZBTB20, STT3B, AFF1, KLHL5, THEMIS, KLF12, NFKB1 
## Negative:  RPL41, RPLP2, RPL13, RPL19, RPLP1, RPS28, RPL27A, RPL28, BANK1, RPS2 
##     RPS18, RPS15, ZEB2, RPL13A, PTK2, HLA-DRA, ARHGAP24, RPL37, RPS12, RPL11 
## PC_ 2 
## Positive:  LINC02694, IKZF2, CCDC141, TOX, STAM, AC093865.1, CDHR3, AC013652.1, TTN, RTKN2 
##     MIR181A1HG, DUSP10, ATXN7L1, ZC2HC1A, SNED1, AC011997.1, LDLRAD4, CEP128, PALM2-AKAP2, SLC1A4 
## Negative:  ANK3, THEMIS, ITGA4, BACH2, NELL2, PRKCA, NR3C2, PDE4D, SBF2, RBMS1 
##     PRKN, PELI2, MYBL1, ADAM23, PLCB1, INPP4B, STAT4, CDK6, UST, DPP4 
## PC_ 3 
## Positive:  SLC16A1-AS1, SKAP1, CORO2A, FOXP1, SPPL3, FUT10, BTBD11, MB21D2, ATF7, ACYP2 
##     ANXA4, TMEM182, EFCAB5, GLUD1, TTN, NINJ2, CUBN, ABHD3, DRAM1, DLGAP1 
## Negative:  RPL11, RPS19, RPS2, RPL3, RPL18A, AC079793.1, RPL13, RPL28, RPLP2, RPL38 
##     RPS15, TPT1, RPL13A, RPL19, EEF1A1, RPL23, RPLP1, RPS18, RPS28, RPL27A 
## PC_ 4 
## Positive:  RPL38, PRKCA, RPL27A, TRBC1, TMSB10, PLCL1, RPS2, LEF1, TPT1, EEF1A1 
##     KANK1, INPP4B, RPL13A, RPL28, TRAT1, IL32, RPS18, RPL37, CRIP1, TSHZ2 
## Negative:  TBC1D9, CDK14, SETBP1, EBF1, BANK1, LYN, OSBPL10, TCF4, ZEB2, JCHAIN 
##     MS4A1, AFF3, HDAC9, IGKC, LRRK2, ARHGAP24, MEF2C, HLA-DQA1, FCRL1, STK33 
## PC_ 5 
## Positive:  PLCB1, LINC00299, ABCB1, SLC4A10, LINC01644, PPP2R2B, NCALD, SAMD3, SYTL2, PDGFD 
##     MYBL1, RUNX2, PDE4D, AL136456.1, TMCC3, AGAP1, NTN4, ADAM12, NEDD4, IL12RB2 
## Negative:  TSHZ2, FHIT, SESN3, ESR1, LEF1, JAM3, CDK14, TBC1D9, FAAH2, TRIO 
##     APP, IL6ST, JCHAIN, AC139720.1, CERS6, USP6NL, LINC01362, RALGPS2, AL353660.1, KCNQ5 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1  0.00879  3.260         0.8980 116.0000  1.16e+02 124.000
## 2      2  0.00183 -0.698         0.9080  60.3000  6.02e+01  69.000
## 3      3  0.02490 -1.690         0.9600  31.9000  3.17e+01  39.100
## 4      4  0.01970 -1.060         0.9710  17.1000  1.70e+01  22.500
## 5      5  0.01460 -0.596         0.9290   9.3300  9.19e+00  13.100
## 6      6  0.07400 -0.805         0.8310   5.1900  4.98e+00   7.930
## 7      7  0.29500 -1.340         0.8970   2.9500  2.76e+00   5.230
## 8      8  0.59200 -1.660         0.8450   1.7200  1.54e+00   3.570
## 9      9  0.77700 -1.780         0.8880   1.0200  8.73e-01   2.510
## 10    10  0.88700 -1.740         0.9250   0.6240  5.03e-01   1.800
## 11    12  0.93500 -1.550         0.9210   0.2510  1.72e-01   0.978
## 12    14  0.94800 -1.420         0.9330   0.1110  6.12e-02   0.553
## 13    16  0.22200 -2.890         0.0866   0.0536  2.29e-02   0.320
## 14    18  0.79900 -1.270         0.7440   0.0277  9.01e-03   0.210
## 15    20  0.23200 -2.390         0.1270   0.0151  3.49e-03   0.145

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3 
## 178  26  11  11

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $brown
##  [1] "ARHGAP15" "DOCK10"   "MDFIC"    "RBMS1"    "INPP4B"   "ZBTB20"  
##  [7] "STT3B"    "NFKB1"    "PRKCA"    "NR3C2"    "BCL2"    
## 
## $turquoise
##  [1] "RPL41"  "RPLP2"  "RPL13"  "RPL19"  "RPLP1"  "RPS28"  "RPL27A" "RPL28" 
##  [9] "RPS2"   "RPS18"  "RPS15"  "RPL13A" "RPL37"  "RPS12"  "RPL11"  "RPS19" 
## [17] "RPL18A" "TMSB10" "RPL38"  "RPL3"   "TPT1"   "EEF1A1" "RPL23"  "FAU"   
## [25] "TRBC1"  "IL32"  
## 
## $blue
##  [1] "LINC02694"  "IKZF2"      "CCDC141"    "TOX"        "STAM"      
##  [6] "AC093865.1" "CDHR3"      "AC013652.1" "TTN"        "DUSP10"    
## [11] "AC011997.1"
## 
## [1] "5/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $brown
##  [1] "ARHGAP15" "DOCK10"   "MDFIC"    "RBMS1"    "INPP4B"   "ZBTB20"  
##  [7] "STT3B"    "NFKB1"    "PRKCA"    "NR3C2"    "BCL2"    
## 
## $turquoise
##  [1] "RPL41"  "RPLP2"  "RPL13"  "RPL19"  "RPLP1"  "RPS28"  "RPL27A" "RPL28" 
##  [9] "RPS2"   "RPS18"  "RPS15"  "RPL13A" "RPL37"  "RPS12"  "RPL11"  "RPS19" 
## [17] "RPL18A" "TMSB10" "RPL38"  "RPL3"   "TPT1"   "EEF1A1" "RPL23"  "FAU"   
## [25] "TRBC1"  "IL32"  
## 
## $blue
##  [1] "LINC02694"  "IKZF2"      "CCDC141"    "TOX"        "STAM"      
##  [6] "AC093865.1" "CDHR3"      "AC013652.1" "TTN"        "DUSP10"    
## [11] "AC011997.1"
## 
## [1] "5021_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.6384
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50169
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.1971e-15
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  ZEB2, AGAP1, TGFBR3, C1orf21, SETBP1, AOAH, LINC02384, PLCB1, MYO3B, ZFPM2 
##     PPP2R2B, MYBL1, LGR6, AL139383.1, MSC-AS1, MIR4435-2HG, FRMPD3, LINC00299, LYN, SLCO4C1 
## Negative:  INPP4B, ARHGAP15, CD28, PAG1, CDC14A, PRKCA, SERINC5, ANK3, STT3B, RBMS1 
##     TAB2, MBNL1, PDE3B, LEF1, DOCK10, AC139720.1, ADAM19, AC079793.1, GPRIN3, FAAH2 
## PC_ 2 
## Positive:  ZEB2, C1orf21, TGFBR3, PARP8, RABGAP1L, JAZF1, NCALD, PPP2R2B, AGAP1, PDGFD 
##     CBLB, SETBP1, TOX, MIR4435-2HG, LINC02384, EIF4G3, KLRG1, GTDC1, DNAJC1, MYO3B 
## Negative:  TIAM1, SERINC5, LEF1, PRKCA, FAAH2, RCAN3, MB21D2, TSHZ2, TSPAN18, TCF7 
##     PVT1, PATJ, ADAM19, AC139720.1, BCL2, CD28, PLCL1, IL2RA, RPL13, SNED1 
## PC_ 3 
## Positive:  DTL, POLQ, FAM111B, STMN1, RRM2, UHRF1, ORC1, NUSAP1, DIAPH3, MYBL2 
##     RGS12, EXO1, SHCBP1, RAD51, FANCD2, CCNE2, HHLA3, FANCA, CIT, CLSPN 
## Negative:  GTDC1, C1orf21, STAU2, LINC00299, RFX3-AS1, EPSTI1, FRY, MGMT, THEMIS, ARID5B 
##     ST8SIA6, AF165147.1, RBMS1, SLC10A7, RORA, MAP3K8, AC078845.1, TPRG1, ANGEL1, HEATR5A 
## PC_ 4 
## Positive:  RPS6, RPS15, RPS28, RPL28, LTB, RPLP2, RPS23, EEF1A1, RPL13, RPL13A 
##     AC079793.1, RPS2, RPL36A, AC013652.1, RPS19, FAU, CDYL2, RPL18, RPL18A, RPL3 
## Negative:  RSPO4, EDA, JAM3, AP003557.1, AL589693.1, ADTRP, SUCLG2-AS1, REPS2, AKAP6, FZD6 
##     CUBN, PCSK5, LPAR3, IGF1R, NBEA, GLIS3, KANK1, EPHB1, PPFIBP1, BCL2L15 
## PC_ 5 
## Positive:  AC093865.1, IKZF2, KLRC3, KLRK1, KLRC2, MTSS1, TTN, BNC2, CD8A, AC243829.2 
##     CD8B, ATP8B4, LYST, AOAH, PIK3AP1, FZD4-DT, FAM49A, AC104041.1, ARHGAP42, AP003557.1 
## Negative:  PTPRM, LINC00299, PLCB1, ANK3, THEMIS, RORA, FKBP5, MYBL1, LINC01619, NCALD 
##     IL12RB2, BTBD11, ADAM19, PLEKHA5, IL18R1, BCL2, IFNG-AS1, HOMER1, LINC02694, ANTXR2 
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1  0.06680  5.650         0.5090 65.4000  65.20000 69.900
## 2      2  0.17000  4.060         0.6660 34.9000  34.70000 39.500
## 3      3  0.00364  0.402         0.5770 19.0000  18.90000 23.500
## 4      4  0.07020 -1.320         0.7560 10.5000  10.60000 14.800
## 5      5  0.28500 -2.090         0.8700  5.9800   5.88000  9.860
## 6      6  0.15500 -5.380        -0.0500  3.4700   3.38000  6.890
## 7      7  0.18600 -4.820        -0.0108  2.0600   1.98000  5.020
## 8      8  0.24500 -6.440         0.0289  1.2500   1.19000  3.800
## 9      9  0.26400 -5.830         0.0540  0.7730   0.71200  2.950
## 10    10  0.28200 -5.450         0.0773  0.4900   0.42500  2.330
## 11    12  0.31800 -5.620         0.1260  0.2110   0.15900  1.530
## 12    14  0.31600 -5.030         0.1220  0.0992   0.06090  1.040
## 13    16  0.30800 -4.470         0.1110  0.0506   0.02400  0.717
## 14    18  0.28000 -4.280         0.1130  0.0278   0.00988  0.505
## 15    20  0.26900 -3.900         0.0905  0.0163   0.00420  0.360

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  1  2  3  4  5 
## 41 28 27 20 10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 3 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 3 module eigengenes in given set.
## $turquoise
##  [1] "ZEB2"        "AGAP1"       "TGFBR3"      "C1orf21"     "SETBP1"     
##  [6] "AOAH"        "PLCB1"       "MYO3B"       "MYBL1"       "LGR6"       
## [11] "MSC-AS1"     "MIR4435-2HG" "SLCO4C1"     "PIP5K1B"     "CTBP2"      
## [16] "AC243829.2"  "PARP8"       "RABGAP1L"    "NCALD"       "CBLB"       
## [21] "TOX"         "EIF4G3"      "KLRG1"       "DNAJC1"      "JAKMIP2"    
## [26] "TFDP2"       "RFX3-AS1"    "EPSTI1"      "MGMT"        "ST8SIA6"    
## [31] "AF165147.1"  "SLC10A7"     "RORA"        "MAP3K8"      "AC078845.1" 
## [36] "TPRG1"       "ANGEL1"      "HEATR5A"     "SETDB2"      "BTBD9"      
## [41] "MAP2K4"     
## 
## $blue
##  [1] "LINC02384"  "ZFPM2"      "PPP2R2B"    "AL139383.1" "FRMPD3"    
##  [6] "LINC00299"  "LYN"        "CLIP2"      "AL365295.1" "JAZF1"     
## [11] "PDGFD"      "GTDC1"      "THEMIS"     "DTL"        "POLQ"      
## [16] "FAM111B"    "STMN1"      "RRM2"       "UHRF1"      "ORC1"      
## [21] "NUSAP1"     "DIAPH3"     "MYBL2"      "RGS12"      "EXO1"      
## [26] "SHCBP1"     "RAD51"      "FANCD2"     "CCNE2"      "HHLA3"     
## [31] "FANCA"      "CIT"        "CLSPN"      "BRIP1"      "NCAPH"     
## [36] "CENPK"      "VAV2"       "BUB1"      
## 
## $brown
##  [1] "INPP4B"     "ARHGAP15"   "CD28"       "PAG1"       "CDC14A"    
##  [6] "PRKCA"      "SERINC5"    "ANK3"       "STT3B"      "RBMS1"     
## [11] "TAB2"       "MBNL1"      "PDE3B"      "LEF1"       "DOCK10"    
## [16] "AC139720.1" "ADAM19"     "AC079793.1" "GPRIN3"     "FAAH2"     
## [21] "ZBTB20"     "MDFIC"      "PATJ"       "AKT3"       "PLCG2"     
## [26] "TIAM1"      "RCAN3"      "MB21D2"     "TSHZ2"      "TSPAN18"   
## [31] "TCF7"       "PVT1"       "BCL2"       "PLCL1"      "IL2RA"     
## [36] "RPL13"      "SNED1"      "PLXNA4"     "TXK"        "KANK1"     
## [41] "AL589693.1" "EDA"        "STAU2"      "FRY"        "ARID5B"    
## [46] "MALAT1"     "GMDS-DT"   
## 
## [1] "3/10000 permutations failed the Mann-Whitney test."
## [1] "12/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
##  [1] "ZEB2"        "AGAP1"       "TGFBR3"      "C1orf21"     "SETBP1"     
##  [6] "AOAH"        "PLCB1"       "MYO3B"       "MYBL1"       "LGR6"       
## [11] "MSC-AS1"     "MIR4435-2HG" "SLCO4C1"     "PIP5K1B"     "CTBP2"      
## [16] "AC243829.2"  "PARP8"       "RABGAP1L"    "NCALD"       "CBLB"       
## [21] "TOX"         "EIF4G3"      "KLRG1"       "DNAJC1"      "JAKMIP2"    
## [26] "TFDP2"       "RFX3-AS1"    "EPSTI1"      "MGMT"        "ST8SIA6"    
## [31] "AF165147.1"  "SLC10A7"     "RORA"        "MAP3K8"      "AC078845.1" 
## [36] "TPRG1"       "ANGEL1"      "HEATR5A"     "SETDB2"      "BTBD9"      
## [41] "MAP2K4"     
## 
## $blue
##  [1] "LINC02384"  "ZFPM2"      "PPP2R2B"    "AL139383.1" "FRMPD3"    
##  [6] "LINC00299"  "LYN"        "CLIP2"      "AL365295.1" "JAZF1"     
## [11] "PDGFD"      "GTDC1"      "THEMIS"     "DTL"        "POLQ"      
## [16] "FAM111B"    "STMN1"      "RRM2"       "UHRF1"      "ORC1"      
## [21] "NUSAP1"     "DIAPH3"     "MYBL2"      "RGS12"      "EXO1"      
## [26] "SHCBP1"     "RAD51"      "FANCD2"     "CCNE2"      "HHLA3"     
## [31] "FANCA"      "CIT"        "CLSPN"      "BRIP1"      "NCAPH"     
## [36] "CENPK"      "VAV2"       "BUB1"      
## 
## $brown
##  [1] "INPP4B"     "ARHGAP15"   "CD28"       "PAG1"       "CDC14A"    
##  [6] "PRKCA"      "SERINC5"    "ANK3"       "STT3B"      "RBMS1"     
## [11] "TAB2"       "MBNL1"      "PDE3B"      "LEF1"       "DOCK10"    
## [16] "AC139720.1" "ADAM19"     "AC079793.1" "GPRIN3"     "FAAH2"     
## [21] "ZBTB20"     "MDFIC"      "PATJ"       "AKT3"       "PLCG2"     
## [26] "TIAM1"      "RCAN3"      "MB21D2"     "TSHZ2"      "TSPAN18"   
## [31] "TCF7"       "PVT1"       "BCL2"       "PLCL1"      "IL2RA"     
## [36] "RPL13"      "SNED1"      "PLXNA4"     "TXK"        "KANK1"     
## [41] "AL589693.1" "EDA"        "STAU2"      "FRY"        "ARID5B"    
## [46] "MALAT1"     "GMDS-DT"   
## 
## [1] "5037_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.7007
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 6.5654e-16

## PC_ 1 
## Positive:  ARHGAP15, MBNL1, ZBTB20, DPYD, INPP4B, PAG1, CAMK4, RORA, AKT3, PLCL2 
##     ANK3, FOXP1, KLF12, RBMS1, PLCG2, MGAT5, LINC01619, TNFAIP8, FBXL17, GPRIN3 
## Negative:  AC105402.3, GNLY, SLA2, PPARG, RBFOX3, STPG2, CDH4, AOAH, LYN, CCBE1 
##     LHFPL2, RRM2, PIK3AP1, ZEB2, AC020916.1, TTC28, SDK1, GPC6, OSBPL5, LINC02267 
## PC_ 2 
## Positive:  LEF1, TSHZ2, INPP4B, PRKCA, FHIT, AC139720.1, TXK, FAAH2, CMTM8, GNAQ 
##     HIVEP2, MAML2, PLCL1, RASGRF2, BCL2, NELL2, BACH2, SESN3, MAN1C1, AL589693.1 
## Negative:  ZEB2, C1orf21, AOAH, SYNE1, TGFBR3, CMIP, SYTL3, GNLY, CEMIP2, PPP2R2B 
##     LINC02384, ATP8A1, SETBP1, MVB12B, PPP1R16B, SLA2, OSBPL5, PDGFD, YES1, NCALD 
## PC_ 3 
## Positive:  RASGRF2, A2M, ATP10A, PLCB1, TAFA1, AOAH, NELL2, C1orf21, SBF2, SAMD3 
##     IFNG-AS1, MCTP2, APBA2, ITGA4, AC139720.1, PCSK5, AGAP1, PRKN, GNLY, GSAP 
## Negative:  LINC02694, MCF2L2, ENTPD1, PLD1, STAM, PTPN13, PKIA, MIR181A1HG, AL136456.1, AC013652.1 
##     PELI1, ADAM12, CENPE, TANC1, TOP2A, NIBAN1, KIF20B, LDLRAD4, AC093865.1, DUSP4 
## PC_ 4 
## Positive:  IKZF2, AC093865.1, TTN, CCDC141, RTKN2, TOX, LEF1, CDHR3, ENTPD1, SLC16A10 
##     STAM, JAZF1, TAFA2, SGMS1, C1orf112, ATXN7L1, VAV3, FANK1, CKAP2L, TMSB10 
## Negative:  FRY, PTPN13, TANC1, ADAM19, PDE4D, ANK3, MYBL1, RBMS1, LINC02649, ADAM12 
##     PELI2, GAB2, LINC00299, RORA, PRKCA, EML4, KLHL5, RUNX2, BCL2, BTBD11 
## PC_ 5 
## Positive:  KIF11, KIF15, CCNA2, KIF14, CDCA8, E2F7, CENPF, SH3RF2, ECT2, MKI67 
##     KIF23, HJURP, RAD51AP1, KIFC1, NCAPG, CCDC150, CCNB1, CKAP2L, KIF18B, DLGAP5 
## Negative:  RTKN2, STAM, TOX, TTN, LINC02694, CCDC141, AC093865.1, IKZF2, AC013652.1, HPGD 
##     LDLRAD4, SETD7, SLC16A10, FANK1, FOXP3, TAFA2, CASK, SGMS1, PELI1, GLCCI1 
##    Power SFT.R.sq slope truncated.R.sq  mean.k. median.k. max.k.
## 1      1  0.00189 -1.51       0.952000 116.0000  1.16e+02 124.00
## 2      2  0.10700 -4.96       0.951000  60.2000  5.99e+01  69.10
## 3      3  0.11500 -2.84       0.914000  31.6000  3.14e+01  39.20
## 4      4  0.28500 -3.03       0.766000  16.8000  1.66e+01  22.90
## 5      5  0.47300 -3.80       0.551000   9.0100  8.79e+00  14.70
## 6      6  0.28800 -8.85       0.171000   4.9000  4.69e+00  10.10
## 7      7  0.31600 -9.49       0.125000   2.7100  2.53e+00   7.37
## 8      8  0.81500 -3.07       0.828000   1.5300  1.38e+00   5.67
## 9      9  0.17300 -3.61       0.101000   0.8820  7.52e-01   4.56
## 10    10  0.17300 -3.11       0.108000   0.5240  4.16e-01   3.79
## 11    12  0.17600 -3.18       0.035100   0.2060  1.32e-01   2.81
## 12    14  0.09390 -2.22       0.037700   0.0972  4.40e-02   2.21
## 13    16  0.17900 -2.55      -0.000718   0.0552  1.52e-02   1.82
## 14    18  0.19800 -2.30       0.001990   0.0367  5.22e-03   1.53
## 15    20  0.15100 -2.00       0.040300   0.0271  1.80e-03   1.31

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3 
## 171  25  18  11

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $blue
##  [1] "ARHGAP15" "MBNL1"    "ZBTB20"   "DPYD"     "PAG1"     "CAMK4"   
##  [7] "AKT3"     "PLCL2"    "FOXP1"    "PLCG2"    "MGAT5"    "TNFAIP8" 
## [13] "FBXL17"   "GNAQ"     "MDFIC"    "HIVEP2"   "LEF1"     "MAML2"   
## 
## $brown
##  [1] "GNLY"    "SLA2"    "AOAH"    "ZEB2"    "OSBPL5"  "C1orf21" "SYNE1"  
##  [8] "CMIP"    "SYTL3"   "YES1"    "ADGRE5" 
## 
## $turquoise
##  [1] "RRM2"     "TOP2A"    "CKAP2L"   "KIF11"    "KIF15"    "CCNA2"   
##  [7] "KIF14"    "CDCA8"    "E2F7"     "CENPF"    "SH3RF2"   "ECT2"    
## [13] "MKI67"    "KIF23"    "HJURP"    "RAD51AP1" "KIFC1"    "NCAPG"   
## [19] "CCDC150"  "CCNB1"    "KIF18B"   "DLGAP5"   "ANLN"     "POLQ"    
## [25] "CCNF"    
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "39/10000 permutations failed the Mann-Whitney test."
## $blue
##  [1] "ARHGAP15" "MBNL1"    "ZBTB20"   "DPYD"     "PAG1"     "CAMK4"   
##  [7] "AKT3"     "PLCL2"    "FOXP1"    "PLCG2"    "MGAT5"    "TNFAIP8" 
## [13] "FBXL17"   "GNAQ"     "MDFIC"    "HIVEP2"   "LEF1"     "MAML2"   
## 
## $brown
##  [1] "GNLY"    "SLA2"    "AOAH"    "ZEB2"    "OSBPL5"  "C1orf21" "SYNE1"  
##  [8] "CMIP"    "SYTL3"   "YES1"    "ADGRE5" 
## 
## $turquoise
##  [1] "RRM2"     "TOP2A"    "CKAP2L"   "KIF11"    "KIF15"    "CCNA2"   
##  [7] "KIF14"    "CDCA8"    "E2F7"     "CENPF"    "SH3RF2"   "ECT2"    
## [13] "MKI67"    "KIF23"    "HJURP"    "RAD51AP1" "KIFC1"    "NCAPG"   
## [19] "CCDC150"  "CCNB1"    "KIF18B"   "DLGAP5"   "ANLN"     "POLQ"    
## [25] "CCNF"    
## 
## [1] "5021_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.4015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.5002
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.0303e-15
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  CDC14A, ARHGAP15, INPP4B, CAMK4, MBNL1, PAG1, RBMS1, GPRIN3, HIVEP2, MDFIC 
##     LEF1, MTAP, MAP3K1, OXNAD1, SERINC5, ANK3, TNFAIP8, RORA, GNAQ, ADAM19 
## Negative:  ZEB2, TOX2, LYN, SETBP1, AOAH, LINC02384, C1orf21, GNLY, OSBPL5, AC243829.2 
##     PECAM1, PRSS23, PDGFD, AGAP1, CCL5, HULC, TCF7L2, KLRK1, DTHD1, GAS7 
## PC_ 2 
## Positive:  SERINC5, BCL2, ADAM19, PRKCA, TIAM1, LEF1, PAG1, AC139720.1, PVT1, TSHZ2 
##     RCAN3, MYO16, ANK3, PLCL1, TAB2, CAMK4, AL589693.1, MAP3K1, SAMD12, RNF157 
## Negative:  ZEB2, TGFBR3, C1orf21, SYTL2, PPP2R2B, MYO3B, LINC02384, MYBL1, TOX, JAKMIP2 
##     SETBP1, RAP1B, PLCB1, JAZF1, AGAP1, TMCC3, PDGFD, NAA50, EPB41L4A, RABGAP1L 
## PC_ 3 
## Positive:  NR3C2, ADAM23, TAFA1, SBF2, IGF1R, TANC2, PLCB1, MYBL1, PELI2, OCA2 
##     BCL2, C8orf37-AS1, THEMIS, BACH2, CFH, FNDC3B, EDA, EML5, CDK6, EEPD1 
## Negative:  ENTPD1, LINC02694, CCDC141, IL12RB2, LY96, AC011997.1, ABLIM1, DUSP4, GRK3, CCDC50 
##     F5, CDHR3, MIR181A1HG, LINC01727, RTKN2, AC093865.1, ATP11A, IKZF2, AC013652.1, TTN 
## PC_ 4 
## Positive:  TBXAS1, SMAD3, FKBP5, BTBD11, PTPRM, THEMIS, ITGA4, IL18RAP, EAF1, AGPAT4 
##     ANK3, NCALD, ST8SIA1, PTPN13, XYLT1, TP63, RORA, TSPAN18, ECT2, NIPSNAP3A 
## Negative:  IKZF2, CDHR3, AC093865.1, CCDC141, SGMS1, CRYZ, AC022075.1, IL2RA, AL136441.1, RTKN2 
##     PLCL1, TAFA2, KLRC4, LINC01727, KLRC3, IRF4, SLC16A10, TTN, GRIP1, KLRK1 
## PC_ 5 
## Positive:  CDIP1, MAPK3, SRGAP3, A2M, AC013652.1, ABHD15-AS1, EAF1, LSM4, AL161457.2, STRADB 
##     CENPI, AP002336.2, MXI1, PLCG2, ARG2, GALNT3, IPO11, LINC00612, ACVR1C, IL18RAP 
## Negative:  KLRC3, AC243829.2, BNC2, HPRT1, MIR181A1HG, PPM1L, DISC1FP1, GOLPH3L, SNX30, FSD1L 
##     TMEM156, OPHN1, CTBP2, PLXNA4, EFNA5, MTSS1, KLRC2, KLRK1, RFX8, SLC12A2 
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k.  max.k.
## 1      1   0.1960 41.900         0.0358 65.8000  65.80000 71.6000
## 2      2   0.2760  4.580         0.8040 35.3000  34.90000 41.4000
## 3      3   0.2960  2.930         0.8380 19.4000  19.10000 25.0000
## 4      4   0.1630  1.440         0.9190 10.9000  10.60000 15.6000
## 5      5   0.0131  0.289         0.8840  6.2700   5.95000  9.9700
## 6      6   0.0037 -0.112         0.8030  3.6800   3.47000  6.5100
## 7      7   0.0186 -0.213         0.7990  2.2100   2.10000  4.3200
## 8      8   0.0455 -0.308         0.6800  1.3500   1.27000  2.9100
## 9      9   0.2860 -0.795         0.6090  0.8370   0.77900  2.0200
## 10    10   0.5190 -1.130         0.7290  0.5280   0.47800  1.4800
## 11    12   0.7670 -1.480         0.8650  0.2190   0.19300  0.8130
## 12    14   0.2550 -3.490         0.1500  0.0957   0.07740  0.4600
## 13    16   0.3050 -4.560         0.2130  0.0436   0.03230  0.2660
## 14    18   0.3640 -5.520         0.2330  0.0207   0.01390  0.1570
## 15    20   0.3690 -5.280         0.2480  0.0102   0.00599  0.0947

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  0  1  2  3  4 
## 26 35 30 21 15

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $blue
##  [1] "CDC14A"     "ARHGAP15"   "INPP4B"     "CAMK4"      "MBNL1"     
##  [6] "PAG1"       "RBMS1"      "GPRIN3"     "HIVEP2"     "MDFIC"     
## [11] "LEF1"       "MTAP"       "MAP3K1"     "OXNAD1"     "SERINC5"   
## [16] "ANK3"       "TNFAIP8"    "RORA"       "GNAQ"       "ADAM19"    
## [21] "TTC39C"     "ZEB1"       "TAB2"       "MAML2"      "PRKCA"     
## [26] "BCL2"       "TIAM1"      "AC139720.1" "PVT1"       "TSHZ2"     
## [31] "RCAN3"      "MYO16"      "AL589693.1" "SAMD12"     "RNF157"    
## [36] "KCNQ1"      "MB21D2"     "FAAH2"      "CD28"       "DPP4"      
## [41] "NR3C2"      "ADAM23"     "SBF2"       "IGF1R"      "PELI2"     
## [46] "BACH2"      "EDA"        "EML5"       "CDK6"       "EEPD1"     
## [51] "ZNF208"    
## 
## $turquoise
##  [1] "ZEB2"       "LYN"        "SETBP1"     "AOAH"       "LINC02384" 
##  [6] "C1orf21"    "GNLY"       "OSBPL5"     "AC243829.2" "PECAM1"    
## [11] "PRSS23"     "PDGFD"      "AGAP1"      "CCL5"       "TCF7L2"    
## [16] "KLRK1"      "DTHD1"      "GAS7"       "TGFBR3"     "EFNA5"     
## [21] "EPB41L4A"   "KCNQ5"      "SYTL2"      "PPP2R2B"    "MYO3B"     
## [26] "MYBL1"      "TOX"        "JAKMIP2"    "PLCB1"      "JAZF1"     
## [31] "TMCC3"      "NAA50"      "RABGAP1L"   "MCTP2"      "EIF4G3"    
## 
## $yellow
##  [1] "PLCL1"      "CCDC141"    "IL12RB2"    "LY96"       "GRK3"      
##  [6] "F5"         "CDHR3"      "MIR181A1HG" "LINC01727"  "RTKN2"     
## [11] "AC093865.1" "IKZF2"      "TTN"        "STAM"       "AHRR"      
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
##  [1] "CDC14A"     "ARHGAP15"   "INPP4B"     "CAMK4"      "MBNL1"     
##  [6] "PAG1"       "RBMS1"      "GPRIN3"     "HIVEP2"     "MDFIC"     
## [11] "LEF1"       "MTAP"       "MAP3K1"     "OXNAD1"     "SERINC5"   
## [16] "ANK3"       "TNFAIP8"    "RORA"       "GNAQ"       "ADAM19"    
## [21] "TTC39C"     "ZEB1"       "TAB2"       "MAML2"      "PRKCA"     
## [26] "BCL2"       "TIAM1"      "AC139720.1" "PVT1"       "TSHZ2"     
## [31] "RCAN3"      "MYO16"      "AL589693.1" "SAMD12"     "RNF157"    
## [36] "KCNQ1"      "MB21D2"     "FAAH2"      "CD28"       "DPP4"      
## [41] "NR3C2"      "ADAM23"     "SBF2"       "IGF1R"      "PELI2"     
## [46] "BACH2"      "EDA"        "EML5"       "CDK6"       "EEPD1"     
## [51] "ZNF208"    
## 
## $turquoise
##  [1] "ZEB2"       "LYN"        "SETBP1"     "AOAH"       "LINC02384" 
##  [6] "C1orf21"    "GNLY"       "OSBPL5"     "AC243829.2" "PECAM1"    
## [11] "PRSS23"     "PDGFD"      "AGAP1"      "CCL5"       "TCF7L2"    
## [16] "KLRK1"      "DTHD1"      "GAS7"       "TGFBR3"     "EFNA5"     
## [21] "EPB41L4A"   "KCNQ5"      "SYTL2"      "PPP2R2B"    "MYO3B"     
## [26] "MYBL1"      "TOX"        "JAKMIP2"    "PLCB1"      "JAZF1"     
## [31] "TMCC3"      "NAA50"      "RABGAP1L"   "MCTP2"      "EIF4G3"    
## 
## $yellow
##  [1] "PLCL1"      "CCDC141"    "IL12RB2"    "LY96"       "GRK3"      
##  [6] "F5"         "CDHR3"      "MIR181A1HG" "LINC01727"  "RTKN2"     
## [11] "AC093865.1" "IKZF2"      "TTN"        "STAM"       "AHRR"      
## 
## [1] "5037_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.7205
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50212
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.441e-15
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  MBNL1, ARHGAP15, ZBTB20, PLCG2, INPP4B, PAG1, MAP3K1, SERINC5, RORA, CASK 
##     MGAT5, TBC1D5, CDC14A, STT3B, HIVEP2, ANTXR2, EXOC4, RFX3, PHACTR2, RBMS1 
## Negative:  GNLY, AOAH, COL25A1, AC105402.3, ZEB2, C1orf21, SETBP1, CDH4, CD300A, ADGRG5 
##     RBMS3, RFX2, ARHGAP26, AC243829.2, CLNK, TTC28, KLRD1, SOX5, AC034195.1, ROR2 
## PC_ 2 
## Positive:  TSHZ2, BCL2, MAP3K1, PRKCA, AL589693.1, LEF1, ADAM19, TXK, FAAH2, KANK1 
##     MGAT5, CMTM8, SERINC5, AC139720.1, KLHL5, DUSP16, SAMD12, MAL, LDLRAD4, AL136456.1 
## Negative:  ZEB2, AOAH, TGFBR3, C1orf21, KLRD1, SAMD3, GNLY, ARHGAP26, MVB12B, PPP2R2B 
##     GAB3, SETBP1, OSBPL5, LINC02384, SYTL2, PDGFD, A2M, NCALD, PZP, KLRG1 
## PC_ 3 
## Positive:  IKZF2, LINC02694, AC093865.1, CCDC141, ENTPD1, KNL1, TTN, STAM, AC013652.1, NUSAP1 
##     CTNNAL1, MIR181A1HG, PBK, RRM2, ASPM, NCAPG, DIAPH3, SHCBP1, TOX, SPC25 
## Negative:  ANK3, MYBL1, THEMIS, STAT4, PLCB1, NR3C2, PITPNC1, ITGA4, UST, MCOLN2 
##     PDE4D, PRKCA, RBMS1, RASGRF2, PCSK5, ATP10A, TAFA1, SATB1-AS1, PRKN, PELI2 
## PC_ 4 
## Positive:  RRM2, KIF18B, DIAPH3, SKA1, CDC6, RAD51AP1, FAM111B, STIL, E2F7, NCAPG 
##     PBK, TTK, ANLN, SHCBP1, SPC25, NUSAP1, DTL, CD109, POLQ, CDCA7L 
## Negative:  IKZF2, AC093865.1, TTN, ENTPD1, CCDC141, ST8SIA1, STAM, HPGD, TOX, LINC02694 
##     AF165147.1, FCRL3, CDHR3, RTKN2, DNAH8, GCNT4, HACD1, DUSP4, ST8SIA6, ATXN7L1 
## PC_ 5 
## Positive:  APBA2, AL353660.1, ST8SIA1, FMN1, TRPS1, KCNQ5, TXK, TSHZ2, LINC01362, TMEM45B 
##     CARMIL1, ANKRD55, LEF1, LINC00402, FKBP5, IFNG-AS1, LINC01284, SLC9A9, SESN3, CERS6 
## Negative:  LINC00299, ADAM12, AL136456.1, FRY, MB21D2, SCART1, CCR6, MCF2L2, NIBAN1, DLEU1 
##     RUNX2, EEPD1, PDE4D, AGPAT4, HPGD, MTUS2, AFDN, NCAPG2, ANK1, PLCB1 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k. max.k.
## 1      1   0.2350 -10.70          0.919 102.0000  1.02e+02 111.00
## 2      2   0.1370  -3.78          0.849  54.0000  5.38e+01  63.00
## 3      3   0.0483  -1.23          0.625  28.9000  2.86e+01  36.30
## 4      4   0.3030  -3.03          0.546  15.8000  1.54e+01  23.00
## 5      5   0.2990 -13.40          0.154   8.7800  8.47e+00  15.70
## 6      6   0.3320 -10.40          0.207   5.0000  4.77e+00  11.50
## 7      7   0.4030 -10.60          0.242   2.9200  2.69e+00   8.99
## 8      8   0.4330  -9.22          0.278   1.7500  1.54e+00   7.37
## 9      9   0.4490  -8.74          0.294   1.0900  8.93e-01   6.28
## 10    10   0.4570  -7.78          0.303   0.7030  5.28e-01   5.51
## 11    12   0.4470  -6.48          0.300   0.3310  1.90e-01   4.52
## 12    14   0.2550  -4.05          0.254   0.1860  6.65e-02   3.92
## 13    16   0.2530  -3.50          0.212   0.1230  2.41e-02   3.52
## 14    18   0.2270  -2.96          0.378   0.0925  9.13e-03   3.25
## 15    20   0.2360  -2.78          0.372   0.0760  3.67e-03   3.06

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5 
## 136  17  13  11  11  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 6 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
## $blue
##  [1] "INPP4B"  "MAP3K1"  "SERINC5" "RORA"    "MGAT5"   "ADAM19"  "BCL2"   
##  [8] "PRKCA"   "ANK3"    "CDK6"    "FRY"     "MB21D2"  "SOS1"   
## 
## $brown
##  [1] "GNLY"      "AOAH"      "ZEB2"      "C1orf21"   "KLRD1"     "OSBPL5"   
##  [7] "TGFBR3"    "MVB12B"    "PPP2R2B"   "LINC02384" "PDGFD"    
## 
## $green
##  [1] "IKZF2"      "LINC02694"  "AC093865.1" "CCDC141"    "ENTPD1"    
##  [6] "TTN"        "STAM"       "AC013652.1" "HPGD"       "ZC3H12C"   
## 
## $turquoise
##  [1] "KNL1"      "NUSAP1"    "CTNNAL1"   "PBK"       "RRM2"      "ASPM"     
##  [7] "NCAPG"     "DIAPH3"    "SHCBP1"    "SPC25"     "ARHGAP11A" "KIF18B"   
## [13] "SKA1"      "CDC6"      "RAD51AP1"  "FAM111B"   "STIL"      "E2F7"     
## [19] "TTK"       "ANLN"      "DTL"       "CD109"     "POLQ"      "CDCA7L"   
## [25] "MKI67"     "RACGAP1"   "PCNA"      "CDK1"     
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
##  [1] "INPP4B"  "MAP3K1"  "SERINC5" "RORA"    "MGAT5"   "ADAM19"  "BCL2"   
##  [8] "PRKCA"   "ANK3"    "CDK6"    "FRY"     "MB21D2"  "SOS1"   
## 
## $brown
##  [1] "GNLY"      "AOAH"      "ZEB2"      "C1orf21"   "KLRD1"     "OSBPL5"   
##  [7] "TGFBR3"    "MVB12B"    "PPP2R2B"   "LINC02384" "PDGFD"    
## 
## $green
##  [1] "IKZF2"      "LINC02694"  "AC093865.1" "CCDC141"    "ENTPD1"    
##  [6] "TTN"        "STAM"       "AC013652.1" "HPGD"       "ZC3H12C"   
## 
## $turquoise
##  [1] "KNL1"      "NUSAP1"    "CTNNAL1"   "PBK"       "RRM2"      "ASPM"     
##  [7] "NCAPG"     "DIAPH3"    "SHCBP1"    "SPC25"     "ARHGAP11A" "KIF18B"   
## [13] "SKA1"      "CDC6"      "RAD51AP1"  "FAM111B"   "STIL"      "E2F7"     
## [19] "TTK"       "ANLN"      "DTL"       "CD109"     "POLQ"      "CDCA7L"   
## [25] "MKI67"     "RACGAP1"   "PCNA"      "CDK1"     
## 
## [1] "5009_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.5999
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.7407e-15

## PC_ 1 
## Positive:  GNLY, ZEB2, SETBP1, AC243829.2, KLRK1, C1orf21, CCL5, RBFOX3, AOAH, KLRD1 
##     PRSS23, FAM49A, ADGRG5, ATP8B4, CLNK, MYO3B, PXDNL, SLCO4C1, LINC01505, SYNE1 
## Negative:  ARHGAP15, MBNL1, CAMK4, INPP4B, CDC14A, DPYD, PLCG2, MDFIC, MGAT5, RORA 
##     GPRIN3, RBMS1, HIVEP2, MAML2, SERINC5, ANTXR2, GNAQ, FBXL17, NR3C2, THEMIS 
## PC_ 2 
## Positive:  ANK3, PRKCA, SERINC5, NR3C2, BCL2, NELL2, AC139720.1, LEF1, FAAH2, RASGRF2 
##     INPP4B, PCSK5, TSHZ2, MAN1C1, TXK, BACH2, SAMD12, CMTM8, RNF157, PELI2 
## Negative:  ZEB2, SAMD3, GNLY, TGFBR3, SETBP1, KLRD1, TOX, SYNE1, C12orf75, KLRK1 
##     PDGFD, AOAH, ARHGAP26, ATP8B4, FAM49A, MIR4435-2HG, RRM2, MYO3B, DIAPH3, PLEK 
## PC_ 3 
## Positive:  ZEB2, GNLY, KLRD1, MCTP2, AOAH, KLRK1, PLEK, PDGFD, MYBL1, ATP8B4 
##     SLC4A4, PPP2R2B, FAM49A, SETBP1, A2M, KLRG1, MYO6, MYO3B, ADGRG5, KLRF1 
## Negative:  ASPM, DIAPH3, KIF18B, NCAPG, RRM2, BUB1B, KIF15, CDCA2, CDK1, ANLN 
##     E2F7, E2F8, MKI67, POLQ, TOP2A, GTSE1, KIF4A, KNL1, ESPL1, PCLAF 
## PC_ 4 
## Positive:  LINC02694, STAM, FANK1, AC013652.1, TTN, CCDC141, SNED1, IKZF2, TOX, NIBAN1 
##     CTLA4, IL2RA, CDK14, IL7, AC093865.1, AL136456.1, CDHR3, MCF2L2, CYTOR, PLD1 
## Negative:  KIF18B, RRM2, CDCA2, KIF15, DIAPH3, KIFC1, ANK3, ANLN, E2F7, APBA2 
##     DEPDC1B, BUB1B, DLGAP5, FBXO5, POLQ, CDK1, CDCA8, E2F8, NR3C2, SPC25 
## PC_ 5 
## Positive:  IKZF2, VAV3, AC093865.1, AL353660.1, TXK, SLC16A10, UBASH3B, CDK14, APBA2, SELL 
##     LINC00402, PLCL1, CCDC141, STAM, ATXN7L1, TTN, BACH1, GCNT4, TOX, CDHR3 
## Negative:  FRY, THEMIS, LINC00299, SLF1, SEPTIN11, ANXA1, AC079793.1, RBMS1, RORA, PTPN13 
##     MSC-AS1, PLD1, RUNX2, ITGB1, KIAA0825, TGFBR3, RBPJ, GTDC1, LINC00511, CDK6 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k. max.k.
## 1      1  0.00340 -1.760         0.7810 108.0000  1.08e+02 115.00
## 2      2  0.00704  1.040         0.7050  57.1000  5.65e+01  64.90
## 3      3  0.11000 -2.360         0.5850  30.5000  3.01e+01  38.70
## 4      4  0.36100 -2.870         0.5190  16.6000  1.61e+01  24.40
## 5      5  0.50500 -2.620         0.4620   9.2600  8.74e+00  16.30
## 6      6  0.76500 -2.570         0.6980   5.2900  4.80e+00  11.60
## 7      7  0.81000 -2.350         0.7930   3.1100  2.65e+00   8.68
## 8      8  0.77500 -2.060         0.8150   1.8900  1.49e+00   6.77
## 9      9  0.72000 -1.860         0.7810   1.2000  8.48e-01   5.46
## 10    10  0.20300 -3.310        -0.0249   0.7860  4.89e-01   4.50
## 11    12  0.73200 -1.360         0.7990   0.3820  1.71e-01   3.21
## 12    14  0.78600 -1.140         0.8380   0.2140  5.90e-02   2.45
## 13    16  0.87600 -1.090         0.8890   0.1330  2.06e-02   1.93
## 14    18  0.88200 -1.030         0.8580   0.0887  7.35e-03   1.55
## 15    20  0.91700 -0.998         0.8970   0.0623  2.78e-03   1.27

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5   6   7 
## 105  30  18  13  12  11  11  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 6 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
## $turquoise
##  [1] "GNLY"       "ZEB2"       "SETBP1"     "AC243829.2" "KLRK1"     
##  [6] "C1orf21"    "CCL5"       "RBFOX3"     "AOAH"       "KLRD1"     
## [11] "PRSS23"     "FAM49A"     "ADGRG5"     "ATP8B4"     "MYO3B"     
## [16] "SYNE1"      "RIN3"       "SAMD3"      "TGFBR3"     "C12orf75"  
## [21] "PDGFD"      "ARHGAP26"   "PLEK"       "MYBL1"      "PPP2R2B"   
## [26] "A2M"        "KLRG1"      "DTHD1"      "SYTL2"      "AGAP1"     
## 
## $brown
##  [1] "ARHGAP15"   "MBNL1"      "INPP4B"     "DPYD"       "PLCG2"     
##  [6] "MDFIC"      "RORA"       "RBMS1"      "MAML2"      "SERINC5"   
## [11] "ANTXR2"     "NR3C2"      "THEMIS"     "SSBP2"      "ANK3"      
## [16] "AC079793.1" "PRKCA"      "BCL2"       "NELL2"      "AC139720.1"
## [21] "LEF1"       "RASGRF2"    "MAN1C1"     "TXK"        "BACH2"     
## [26] "SAMD12"     "KCNQ1"      "AC233976.1" "AL353660.1" "SELL"      
## [31] "LINC00402"  "GCNT4"      "PTPN13"     "CDK6"       "ERN1"      
## 
## $blue
##  [1] "RRM2"    "DIAPH3"  "KIFC1"   "POLQ"    "ASPM"    "KIF18B"  "NCAPG"  
##  [8] "BUB1B"   "KIF15"   "CDCA2"   "CDK1"    "ANLN"    "E2F7"    "E2F8"   
## [15] "MKI67"   "TOP2A"   "GTSE1"   "KIF4A"   "KNL1"    "ESPL1"   "PCLAF"  
## [22] "DLGAP5"  "CDCA8"   "SHCBP1"  "STMN1"   "DEPDC1B" "FBXO5"   "SPC25"  
## [29] "CDC25C"  "PLEKHA5"
## 
## $black
##  [1] "STAM"       "FANK1"      "TTN"        "CCDC141"    "CTLA4"     
##  [6] "IL2RA"      "MIR181A1HG" "SLC16A10"   "TSHR"       "RTKN2"     
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "3/10000 permutations failed the Mann-Whitney test."
## $turquoise
##  [1] "GNLY"       "ZEB2"       "SETBP1"     "AC243829.2" "KLRK1"     
##  [6] "C1orf21"    "CCL5"       "RBFOX3"     "AOAH"       "KLRD1"     
## [11] "PRSS23"     "FAM49A"     "ADGRG5"     "ATP8B4"     "MYO3B"     
## [16] "SYNE1"      "RIN3"       "SAMD3"      "TGFBR3"     "C12orf75"  
## [21] "PDGFD"      "ARHGAP26"   "PLEK"       "MYBL1"      "PPP2R2B"   
## [26] "A2M"        "KLRG1"      "DTHD1"      "SYTL2"      "AGAP1"     
## 
## $brown
##  [1] "ARHGAP15"   "MBNL1"      "INPP4B"     "DPYD"       "PLCG2"     
##  [6] "MDFIC"      "RORA"       "RBMS1"      "MAML2"      "SERINC5"   
## [11] "ANTXR2"     "NR3C2"      "THEMIS"     "SSBP2"      "ANK3"      
## [16] "AC079793.1" "PRKCA"      "BCL2"       "NELL2"      "AC139720.1"
## [21] "LEF1"       "RASGRF2"    "MAN1C1"     "TXK"        "BACH2"     
## [26] "SAMD12"     "KCNQ1"      "AC233976.1" "AL353660.1" "SELL"      
## [31] "LINC00402"  "GCNT4"      "PTPN13"     "CDK6"       "ERN1"      
## 
## $blue
##  [1] "RRM2"    "DIAPH3"  "KIFC1"   "POLQ"    "ASPM"    "KIF18B"  "NCAPG"  
##  [8] "BUB1B"   "KIF15"   "CDCA2"   "CDK1"    "ANLN"    "E2F7"    "E2F8"   
## [15] "MKI67"   "TOP2A"   "GTSE1"   "KIF4A"   "KNL1"    "ESPL1"   "PCLAF"  
## [22] "DLGAP5"  "CDCA8"   "SHCBP1"  "STMN1"   "DEPDC1B" "FBXO5"   "SPC25"  
## [29] "CDC25C"  "PLEKHA5"
## 
## $black
##  [1] "STAM"       "FANK1"      "TTN"        "CCDC141"    "CTLA4"     
##  [6] "IL2RA"      "MIR181A1HG" "SLC16A10"   "TSHR"       "RTKN2"     
## 
## [1] "5009_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.2262
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.32308
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 0
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  ARHGAP15, GPRIN3, CD28, INPP4B, DPYD, ELMO1, SERINC5, USP3, MGAT5, EML4 
##     ZBTB20, FAAH2, SMCHD1, STT3B, TTC39C, SFXN1, PDE3B, CAMK4, PDE7A, ADK 
## Negative:  ZEB2, TRBV23-1, RHBDF2, RPS19, RPS27A, GNLY, ATP8B4, SHTN1, C1orf21, C5orf17 
##     RPL41, KLRD1, TFAP2A-AS1, FAM49A, OSBPL5, GSN, ZNF347, LINC02664, MVB12B, LINC00667 
## PC_ 2 
## Positive:  ANK3, LEF1, BCL2, RCAN3, FAAH2, TSHZ2, PRKCA, NELL2, CMTM8, PVT1 
##     ADAM19, SERINC5, PELI2, GNAQ, TTC39C, PAG1, AC139720.1, RASGRF2, TMEM123, AC233976.1 
## Negative:  ZEB2, ARHGAP26, CEP78, AOAH, GNLY, CMIP, SAMD3, C1orf21, TGFBR3, PPP2R2B 
##     SETBP1, MYO3B, NCALD, PPM1L, RABGAP1L, OSBPL5, NAA50, AGAP1, KLRG1, PDGFD 
## PC_ 3 
## Positive:  RAPGEF2, ARHGAP26, SAMD3, NCALD, SSBP3, ARAP2, PTPN12, ZBTB20, PPP2R2B, ANKRD28 
##     NIBAN1, NSMAF, RAP1GDS1, ZEB2, KLRG1, ZNF407, TGFBR3, MYO6, SGMS1, PLEKHA5 
## Negative:  BAD, KIF11, BUB1B, MAP1S, CCNA2, CCNE2, CDCA8, PLXDC1, AGA, POC1A 
##     MLC1, KNL1, IQCH, GDAP1, ZNF16, KPNA2, GPSM2, CENPO, MBOAT2, REXO5 
## PC_ 4 
## Positive:  LINC01588, MRPL50, NR3C2, TFDP2, EFCAB6, AC139720.1, DNAJC6, SINHCAF, AL353660.1, PITPNC1 
##     FBXO38, NEXMIF, RNF19B, ZC4H2, SPECC1L, AC011447.3, OCRL, MAP2K6, TRABD2A, PRKN 
## Negative:  ADAM12, C15orf39, LRP12, AC019117.1, PLD1, RORA-AS1, SNED1, LINC02694, AC104365.1, ELOVL4 
##     AC013652.1, LINC00598, MCF2L2, AL589990.1, ATP13A4, C16orf95, RPS17, TMSB10, ENTPD5, FRY 
## PC_ 5 
## Positive:  TMSB10, AP001011.1, RPL28, ACTG1, AC104365.1, RPS17, GLIPR1, S100A6, AC079793.1, LTB 
##     RPLP2, FOSB, RPL34, SH3BGRL3, ATP6AP1, FAU, JUN, EEF1A1, PRTFDC1, TEX14 
## Negative:  CD80, AC019117.1, NLN, CZIB, TMEM178B, C16orf95, ELOVL4, AC007220.1, MICU3, GSKIP 
##     POLE2, AL096803.2, ANK1, CENPQ, EMC1, AL138720.1, PRKAR1B, CCDC200, CDK6, STPG1 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1 0.000157  0.203         0.6280 111.0000  112.0000 118.000
## 2      2 0.003660  0.529         0.5710  58.8000   59.0000  66.800
## 3      3 0.012500 -0.729         0.6090  31.7000   31.7000  39.300
## 4      4 0.142000 -2.210         0.8030  17.4000   17.4000  24.100
## 5      5 0.234000 -2.440         0.7620   9.7800    9.7600  15.400
## 6      6 0.451000 -2.800         0.8170   5.6100    5.6100  10.300
## 7      7 0.240000 -6.190         0.1780   3.3000    3.3100   7.170
## 8      8 0.267000 -5.510         0.2020   1.9900    1.9700   5.170
## 9      9 0.187000 -4.080        -0.0437   1.2300    1.2000   3.860
## 10    10 0.756000 -2.450         0.7720   0.7780    0.7440   2.950
## 11    12 0.182000 -3.050        -0.0150   0.3370    0.3010   1.850
## 12    14 0.145000 -3.220        -0.0396   0.1610    0.1220   1.240
## 13    16 0.358000 -4.670         0.2390   0.0847    0.0526   0.868
## 14    18 0.285000 -4.340         0.0832   0.0487    0.0240   0.668
## 15    20 0.244000 -3.610         0.0575   0.0303    0.0114   0.559

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3 
## 173  20  12  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $brown
##  [1] "RPS19"  "RPS27A" "RPL41"  "RPS17"  "TMSB10" "FAU"    "RPL28"  "LTB"   
##  [9] "RPLP2"  "RPL34" 
## 
## $turquoise
##  [1] "MAP1S"  "BAD"    "KIF11"  "BUB1B"  "CCNA2"  "CCNE2"  "CDCA8"  "PLXDC1"
##  [9] "MLC1"   "KNL1"   "IQCH"   "GDAP1"  "KPNA2"  "CENPO"  "REXO5"  "POLD1" 
## [17] "ORC1"   "ZNF850" "NDC80"  "FBXO5" 
## 
## $blue
##  [1] "AC019117.1" "ELOVL4"     "LINC00598"  "ATP13A4"    "GSKIP"     
##  [6] "CZIB"       "AC007220.1" "AL096803.2" "CENPQ"      "EMC1"      
## [11] "CCDC200"    "STPG1"     
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1/10000 permutations failed the Mann-Whitney test."
## $brown
##  [1] "RPS19"  "RPS27A" "RPL41"  "RPS17"  "TMSB10" "FAU"    "RPL28"  "LTB"   
##  [9] "RPLP2"  "RPL34" 
## 
## $turquoise
##  [1] "MAP1S"  "BAD"    "KIF11"  "BUB1B"  "CCNA2"  "CCNE2"  "CDCA8"  "PLXDC1"
##  [9] "MLC1"   "KNL1"   "IQCH"   "GDAP1"  "KPNA2"  "CENPO"  "REXO5"  "POLD1" 
## [17] "ORC1"   "ZNF850" "NDC80"  "FBXO5" 
## 
## $blue
##  [1] "AC019117.1" "ELOVL4"     "LINC00598"  "ATP13A4"    "GSKIP"     
##  [6] "CZIB"       "AC007220.1" "AL096803.2" "CENPQ"      "EMC1"      
## [11] "CCDC200"    "STPG1"     
## 
## [1] "5003_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.3748
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.32366
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 7.2183e-31
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  ARHGAP15, RORA, LRRC8C, MBNL1, DPYD, ZBTB20, CELF2, ANKRD44, LINC01619, ELMO1 
##     RUNX1, PARP8, SP3, KLF12, MCTP2, TCF12, TGFBR3, RBMS1, INPP4B, NIBAN1 
## Negative:  RPS18, RPL13, RPLP1, RPL39, RPS27, RPL41, RPS28, RPS12, RPL11, RPL34 
##     RPL32, RPL9, RPL23, RPS21, RPL8, RPL23A, RPL37A, RPL35, RPS2, RPL10 
## PC_ 2 
## Positive:  C1orf21, ZEB2, PDGFD, GNLY, MAP3K8, PPP2R2B, AGPAT4, SGCD, PROK2, VAV3 
##     SYNE1, LINC02384, ETHE1, MSC-AS1, ARHGEF12, RGS3, PLXND1, SLC4A8, NDUFB6, TMCC3 
## Negative:  RPL13, ANK3, RPL34, RPS2, INPP4B, RPL39, RPS12, RPL21, CDC14A, RPL41 
##     RPL23, RPL30, RPLP1, RPS18, RPS27, RPL37A, RPS28, RPL11, RPL35, SERINC5 
## PC_ 3 
## Positive:  CCDC141, TSHR, IKZF2, FOXP3, AC093865.1, LINC02694, LINC00426, TOX, STAM, RTKN2 
##     TTN, LYRM1, SLC16A10, CDHR3, MIR181A1HG, CTLA4, ST8SIA4, FANK1, ENTPD1, ATXN7L1 
## Negative:  PLCB1, PDGFD, C1orf21, GNLY, MYBL1, ZEB2, MCTP2, PTPRM, LINC02384, ANK3 
##     CASC8, PROK2, PAFAH2, THEMIS, PELI2, NDUFB6, ARHGAP26, ATP10A, SGCD, SYTL2 
## PC_ 4 
## Positive:  RPS28, RPL37A, RPL41, RPS2, RPL34, RPL11, RPL39, RPS21, RPLP1, RPS27 
##     RPS18, RPL10, RPL23, RPS12, RPS15, RPL30, RPL9, RPL13, RPL18, RPL23A 
## Negative:  TMEM131L, CCND3, CERS6, FHIT, PRKCA, ITPKB, TSHZ2, KCNQ1, SGK3, ASCC1 
##     ATP11C, SNAI3-AS1, ZBTB26, CMTM8, AL589693.1, Z94721.1, ZNF710, AC040934.1, PRKAG2, UNC50 
## PC_ 5 
## Positive:  TTLL7, FAM214B, C5orf30, GCA, FRY, MAML3, BHLHE40-AS1, KIAA0825, TMEM200A, ZNF418 
##     UFL1-AS1, SMIM12, AC008014.1, COL24A1, DSCAML1, IATPR, PKP4, ZNF81, MMRN1, ANKRD28 
## Negative:  IER3IP1, Z98884.1, ADAL, AC084125.2, CERS6, TRMT11, GCNT2, RGL1, YAE1, METTL8 
##     SNX30, ZNF627, CLN6, RNLS, AC007262.2, GRPEL2, MRC2, MCM8, POLD3, EXT1 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1  0.03100  6.090        0.85600 118.0000  118.0000 125.000
## 2      2  0.05240  4.110        0.75200  61.7000   61.3000  68.600
## 3      3  0.04370  2.330        0.85200  32.6000   32.4000  38.100
## 4      4  0.00667  0.666        0.88600  17.5000   17.4000  21.900
## 5      5  0.03550 -1.170        0.90200   9.5600    9.4700  13.000
## 6      6  0.07580 -1.320        0.79500   5.3200    5.2300   7.960
## 7      7  0.24200 -1.680        0.87500   3.0100    2.9200   5.030
## 8      8  0.52100 -2.150        0.88500   1.7500    1.6700   3.490
## 9      9  0.65500 -2.230        0.87600   1.0400    0.9500   2.510
## 10    10  0.81000 -2.290        0.90000   0.6320    0.5500   1.840
## 11    12  0.91300 -1.960        0.93400   0.2530    0.1950   1.040
## 12    14  0.92900 -1.830        0.91100   0.1130    0.0702   0.656
## 13    16  0.22600 -2.850        0.00466   0.0551    0.0264   0.501
## 14    18  0.28100 -3.660        0.08700   0.0293    0.0109   0.397
## 15    20  0.29100 -3.910        0.08790   0.0167    0.0045   0.323

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3 
## 179  26  15  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $turquoise
##  [1] "RPS18"  "RPL13"  "RPLP1"  "RPL39"  "RPS27"  "RPL41"  "RPS28"  "RPS12" 
##  [9] "RPL11"  "RPL34"  "RPL32"  "RPL9"   "RPL23"  "RPS21"  "RPL8"   "RPL23A"
## [17] "RPL37A" "RPL35"  "RPS2"   "RPL10"  "RPL18"  "RPL30"  "RPL12"  "RPL21" 
## [25] "RPS15"  "RPS3"  
## 
## $brown
##  [1] "C1orf21"   "ZEB2"      "PDGFD"     "GNLY"      "PPP2R2B"   "AGPAT4"   
##  [7] "SYNE1"     "LINC02384" "TMCC3"     "PLCB1"    
## 
## $blue
##  [1] "TTLL7"    "GCA"      "TMEM200A" "SMIM12"   "COL24A1"  "DSCAML1" 
##  [7] "MMRN1"    "GPR82"    "MYO16"    "RRAGD"    "DPF3"     "TMEM67"  
## [13] "LY86"     "ADAM23"   "DCBLD1"  
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
##  [1] "RPS18"  "RPL13"  "RPLP1"  "RPL39"  "RPS27"  "RPL41"  "RPS28"  "RPS12" 
##  [9] "RPL11"  "RPL34"  "RPL32"  "RPL9"   "RPL23"  "RPS21"  "RPL8"   "RPL23A"
## [17] "RPL37A" "RPL35"  "RPS2"   "RPL10"  "RPL18"  "RPL30"  "RPL12"  "RPL21" 
## [25] "RPS15"  "RPS3"  
## 
## $brown
##  [1] "C1orf21"   "ZEB2"      "PDGFD"     "GNLY"      "PPP2R2B"   "AGPAT4"   
##  [7] "SYNE1"     "LINC02384" "TMCC3"     "PLCB1"    
## 
## $blue
##  [1] "TTLL7"    "GCA"      "TMEM200A" "SMIM12"   "COL24A1"  "DSCAML1" 
##  [7] "MMRN1"    "GPR82"    "MYO16"    "RRAGD"    "DPF3"     "TMEM67"  
## [13] "LY86"     "ADAM23"   "DCBLD1"  
## 
## [1] "5003_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.3214
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49966
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 8.8442e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  RBMS1, ARHGAP15, PIP4K2A, PARP8, CBLB, MBNL1, SSH2, STK39, PPP3CA, CELF2 
##     ZBTB20, PHACTR2, CATSPERB, PAG1, GRAMD2B, FBXO11, MAML2, UMAD1, ANTXR2, SLC16A7 
## Negative:  TMSB10, HLA-C, TMSB4X, JUN, FOS, GAPDH, MALAT1, AC022217.3, UQCRB, CCDC141 
##     IKZF2, BTF3, IL5RA, TTN, TPI1, LGALS1, S100A4, LINC02422, ARL4A, CSKMT 
## PC_ 2 
## Positive:  PRKCA, ANK3, INPP4B, CDC14A, DOCK10, MDFIC, DENND5A, NELL2, ARHGAP15, AC139720.1 
##     MGAT5, BCL2, TSHZ2, HIVEP2, RBMS1, PCSK5, RASGRF2, PITPNC1, KCNQ1, APBA2 
## Negative:  TOX, ZEB2, PDGFD, C1orf21, TRGC2, AC093865.1, VAV3, NDUFAF4, IKZF2, PEX5 
##     EPB41L4A, PGPEP1, ADGRG1, HLA-DRB1, KLRK1, DMXL2, CMKLR1, ATP6V0A1, LINC02694, PPP2R2B 
## PC_ 3 
## Positive:  LINC02694, STAM, ENTPD1, IKZF2, AC013652.1, AC093865.1, RTKN2, PLCL1, MAP3K1, F5 
##     HMCN1, S100A4, IL2RA, TTN, CDHR3, DLEU7, SNED1, PALM2-AKAP2, TAFA2, GPA33 
## Negative:  PDGFD, C1orf21, ZEB2, PITPNC1, TRGC2, PLCB1, THEMIS, PTPRM, EPB41L4A, KLRK1 
##     PTGDR, GNLY, SAMD3, MCOLN2, DTHD1, AGAP1, AOAH, IL18RAP, GAS7, MYO6 
## PC_ 4 
## Positive:  SH3RF3, EDAR, RHCE, SGO2, ANKRD24, FBXL14, PACRG, NEBL, AC092535.4, AGPAT5 
##     AC119403.1, EEF1AKMT1, SNX18, ACER1, TULP4, ALDH8A1, PTPA, GCNT2, AC079447.1, WNT5B 
## Negative:  FRY, SLC13A3, ZNF570, RUNX2, MSC-AS1, EEPD1, MB21D2, ABCB1, AUTS2, LINC02694 
##     DTHD1, PKIA, LMNA, CPNE8, HTRA4, SEPTIN11, CMC1, PTPN13, HDGFL3, CIITA 
## PC_ 5 
## Positive:  BAALC-AS1, DRD3, ZNF570, HDX, DMPK, NEK10, TMED3, TPTE2, AC024028.1, SLC13A3 
##     LINC01727, NECTIN3, HEATR9, WDR63, RBBP8, ZDHHC7, AC009315.1, EPB41L2, DNMBP, DTHD1 
## Negative:  HLA-C, TNFAIP3, PLCB1, EMILIN2, LMNA, IFNG-AS1, FOS, ERLIN1, COX8A, WAKMAR2 
##     SEMA4A, HBS1L, IL32, JAM3, AP4M1, BTG3, PACSIN1, IL12RB2, SPIRE1, C4orf33 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1  0.23100 16.800         0.8030 92.10000  92.40000 96.5000
## 2      2  0.24600  8.710         0.6820 48.00000  48.40000 52.5000
## 3      3  0.41200  7.270         0.8490 25.40000  25.60000 28.8000
## 4      4  0.38700  5.070         0.8160 13.60000  13.70000 16.2000
## 5      5  0.17900 12.100         0.0547  7.38000   7.41000  9.4700
## 6      6  0.03290  0.964         0.4970  4.07000   4.04000  5.7200
## 7      7  0.00357 -0.240         0.7620  2.29000   2.26000  3.5600
## 8      8  0.02900 -0.561         0.8170  1.31000   1.26000  2.2900
## 9      9  0.09020 -0.843         0.8590  0.76500   0.72300  1.5200
## 10    10  0.14900 -0.937         0.9180  0.45600   0.41900  1.0400
## 11    12  0.38300 -1.250         0.8370  0.17300   0.14600  0.5280
## 12    14  0.25900 -3.970         0.1540  0.07180   0.05170  0.2920
## 13    16  0.92700 -1.780         0.9310  0.03260   0.01970  0.1720
## 14    18  0.87800 -1.660         0.8470  0.01610   0.00765  0.1060
## 15    20  0.09780 -1.780        -0.0660  0.00853   0.00317  0.0669

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  0  1  2  3  4  5  6  7 
## 83 22 19 12 12 11 11 10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 6 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 6 module eigengenes in given set.
## $yellow
##  [1] "RBMS1"      "ARHGAP15"   "PIP4K2A"    "PARP8"      "CBLB"      
##  [6] "MBNL1"      "PPP3CA"     "CELF2"      "ZBTB20"     "MAML2"     
## [11] "UMAD1"      "ANTXR2"     "SLC4A7"     "STAT4"      "PRKCA"     
## [16] "ANK3"       "INPP4B"     "CDC14A"     "DOCK10"     "MDFIC"     
## [21] "NELL2"      "AC139720.1" "MGAT5"      "BCL2"       "HIVEP2"    
## [26] "PCSK5"      "RASGRF2"    "PITPNC1"    "KCNQ1"      "PRKN"      
## [31] "MAN1C1"     "SBF2"       "THEMIS"     "MB21D2"    
## 
## $green
##  [1] "TMSB10"     "HLA-C"      "TMSB4X"     "GAPDH"      "UQCRB"     
##  [6] "BTF3"       "LGALS1"     "S100A4"     "AC087286.2" "IL32"      
## [11] "HLA-DRB1"  
## 
## $blue
##  [1] "CCDC141"     "IKZF2"       "TTN"         "TOX"         "AC093865.1" 
##  [6] "VAV3"        "LINC02694"   "AC013652.1"  "STAM"        "RTKN2"      
## [11] "PLCL1"       "IL2RA"       "CDHR3"       "DLEU7"       "SNED1"      
## [16] "PALM2-AKAP2" "TAFA2"       "AL136456.1"  "MSC-AS1"    
## 
## $red
##  [1] "ZEB2"     "KLRK1"    "ACSL1"    "MCOLN2"   "AOAH"     "ALDH18A1"
##  [7] "DMPK"     "TRGC1"    "SLC4A4"   "SLC13A3"  "CIITA"   
## 
## $turquoise
##  [1] "SH3RF3"     "EDAR"       "RHCE"       "SGO2"       "ANKRD24"   
##  [6] "FBXL14"     "PACRG"      "NEBL"       "AC092535.4" "AGPAT5"    
## [11] "AC119403.1" "EEF1AKMT1"  "SNX18"      "ACER1"      "ALDH8A1"   
## [16] "PTPA"       "GCNT2"      "AC079447.1" "WNT5B"      "SDHD"      
## [21] "AL353660.1" "EPN2"      
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $yellow
##  [1] "RBMS1"      "ARHGAP15"   "PIP4K2A"    "PARP8"      "CBLB"      
##  [6] "MBNL1"      "PPP3CA"     "CELF2"      "ZBTB20"     "MAML2"     
## [11] "UMAD1"      "ANTXR2"     "SLC4A7"     "STAT4"      "PRKCA"     
## [16] "ANK3"       "INPP4B"     "CDC14A"     "DOCK10"     "MDFIC"     
## [21] "NELL2"      "AC139720.1" "MGAT5"      "BCL2"       "HIVEP2"    
## [26] "PCSK5"      "RASGRF2"    "PITPNC1"    "KCNQ1"      "PRKN"      
## [31] "MAN1C1"     "SBF2"       "THEMIS"     "MB21D2"    
## 
## $green
##  [1] "TMSB10"     "HLA-C"      "TMSB4X"     "GAPDH"      "UQCRB"     
##  [6] "BTF3"       "LGALS1"     "S100A4"     "AC087286.2" "IL32"      
## [11] "HLA-DRB1"  
## 
## $blue
##  [1] "CCDC141"     "IKZF2"       "TTN"         "TOX"         "AC093865.1" 
##  [6] "VAV3"        "LINC02694"   "AC013652.1"  "STAM"        "RTKN2"      
## [11] "PLCL1"       "IL2RA"       "CDHR3"       "DLEU7"       "SNED1"      
## [16] "PALM2-AKAP2" "TAFA2"       "AL136456.1"  "MSC-AS1"    
## 
## $red
##  [1] "ZEB2"     "KLRK1"    "ACSL1"    "MCOLN2"   "AOAH"     "ALDH18A1"
##  [7] "DMPK"     "TRGC1"    "SLC4A4"   "SLC13A3"  "CIITA"   
## 
## $turquoise
##  [1] "SH3RF3"     "EDAR"       "RHCE"       "SGO2"       "ANKRD24"   
##  [6] "FBXL14"     "PACRG"      "NEBL"       "AC092535.4" "AGPAT5"    
## [11] "AC119403.1" "EEF1AKMT1"  "SNX18"      "ACER1"      "ALDH8A1"   
## [16] "PTPA"       "GCNT2"      "AC079447.1" "WNT5B"      "SDHD"      
## [21] "AL353660.1" "EPN2"      
## 
## [1] "5016_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.538
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50061
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 6.8257e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  CAMK4, LEF1, PRKCA, SERINC5, INPP4B, ANK3, TSHZ2, HIVEP2, MAML2, CDC14A 
##     MAP3K1, PAG1, CSGALNACT1, CD28, GNAQ, TTC39C, PDE3B, MGAT5, ZEB1, PLCL1 
## Negative:  AOAH, ZEB2, AC243829.2, C1orf21, TGFBR3, GNLY, PPP2R2B, SAMD3, KLRD1, ARHGAP26 
##     SETBP1, VAV3, SGCD, DTHD1, LINC02384, OSBPL5, KLRG1, MCTP2, JAZF1, AL392086.3 
## PC_ 2 
## Positive:  RPLP1, RPLP2, RPL13, RPL28, RPL41, RPS2, RPL3, RPL13A, RPL19, RPL10A 
##     FAU, RPL30, FOS, EEF1A1, JUN, FOSB, DNAJA1, JUNB, AC022217.3, TUBA1A 
## Negative:  CHST11, RORA, KLF12, PPP1R16B, GPRIN3, ARHGAP15, MAP3K5, CD247, LINC00944, RUNX1 
##     GALNT1, NIBAN1, JAZF1, SAMD3, OSBPL3, PPP2R2B, PAM, PRR5L, HIVEP3, SLC9A9 
## PC_ 3 
## Positive:  UBASH3B, MAML3, SLC16A10, AC106795.3, CD28, SH3RF3, LINC01550, LINC01135, NAV1, AC139720.1 
##     FRMD3, PRKCA, GCNT4, AL589693.1, IL2RA, APOLD1, SERTAD2, LINC01483, ZNRF1, LYRM9 
## Negative:  JUN, FOS, FOSB, RPL3, DNAJA1, JUNB, RPS2, RPL13A, DDX3Y, SLC38A2 
##     TEX14, RPL10A, FAU, RPL41, AL606489.1, RPLP2, IFRD1, IER5, AC022217.3, RPL28 
## PC_ 4 
## Positive:  LINC02694, AC013652.1, KIAA0825, MSC-AS1, NIBAN1, HPGD, BCL2L11, DLEU2, CHDH, PARP2 
##     HHAT, RTKN2, GNB4, DUSP10, CENPP, OSBPL1A, SNED1, E2F3, PAG1, MCF2L2 
## Negative:  TXK, IGF1R, CERS6, PCSK5, OSBPL5, ARHGAP32, SAMD12, PRKN, EPB41L4A, NCAM1 
##     CMTM8, PELI2, AL392086.3, ZNF146, AC233976.1, KANK1, SATB1-AS1, GNLY, KLRF1, KLRC3 
## PC_ 5 
## Positive:  THEMIS, ITGA4, IFNG-AS1, CMC1, AL590006.1, TRPS1, PRKCB, LINC01934, LINC02725, NELL2 
##     ST8SIA1, SBF2, WHRN, E2F3, TASP1, CBLB, AC243829.1, AC006369.1, MYOM1, GZMK 
## Negative:  CTBP2, FRY, LINC00511, LINC02694, CERNA1, PLD1, ZBTB16, SNED1, MIR646HG, AC013652.1 
##     HPGD, AC005237.1, CSGALNACT1, EGLN3, SEMA5A, RTKN2, AC122685.1, BNC2, TXNDC5, ADCK1 
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1 1.55e-05 -0.155         0.8790 84.3000  84.40000 88.200
## 2      2 2.04e-01  8.970         0.8650 43.8000  43.50000 47.700
## 3      3 1.01e-01  2.930         0.7480 23.3000  23.20000 27.000
## 4      4 3.36e-02  0.824         0.8640 12.7000  12.50000 16.200
## 5      5 1.22e-01 -1.190         0.8650  7.0900   6.86000 10.800
## 6      6 4.95e-01 -1.970         0.8040  4.0700   3.88000  7.630
## 7      7 7.36e-01 -2.000         0.8210  2.4100   2.20000  5.570
## 8      8 8.93e-01 -2.010         0.9240  1.4700   1.27000  4.170
## 9      9 9.21e-01 -1.830         0.9090  0.9290   0.73700  3.190
## 10    10 9.47e-01 -1.700         0.9320  0.6030   0.43400  2.480
## 11    12 8.04e-01 -1.520         0.7610  0.2780   0.15800  1.540
## 12    14 8.56e-01 -1.370         0.8260  0.1410   0.05790  0.991
## 13    16 8.22e-01 -1.240         0.8140  0.0778   0.02210  0.668
## 14    18 9.87e-02 -1.540        -0.0639  0.0455   0.00864  0.465
## 15    20 1.60e-01 -1.860        -0.0738  0.0279   0.00358  0.327

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  0  1  2  3  4  5 
## 93 18 15 15 13 13

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 6 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $turquoise
##  [1] "CAMK4"      "LEF1"       "PRKCA"      "SERINC5"    "INPP4B"    
##  [6] "ANK3"       "TSHZ2"      "HIVEP2"     "MAML2"      "CDC14A"    
## [11] "MAP3K1"     "PAG1"       "CSGALNACT1" "GNAQ"       "TTC39C"    
## [16] "PDE3B"      "MGAT5"      "ZEB1"       "PLCL1"      "RASGRF2"   
## [21] "TMEM123"    "FAAH2"      "EPHA4"      "ARHGAP15"   "ZBTB20"    
## [26] "AC139720.1" "PCSK5"      "SAMD12"     "CMTM8"      "AC233976.1"
## [31] "SATB1-AS1" 
## 
## $blue
##  [1] "AOAH"       "ZEB2"       "AC243829.2" "C1orf21"    "TGFBR3"    
##  [6] "PPP2R2B"    "SAMD3"      "ARHGAP26"   "VAV3"       "DTHD1"     
## [11] "LINC02384"  "AL392086.3" "CMIP"       "HIVEP3"     "SYTL2"     
## 
## $brown
##  [1] "RPLP1"      "RPLP2"      "RPL13"      "RPL28"      "RPL41"     
##  [6] "RPS2"       "RPL3"       "RPL13A"     "RPL19"      "RPL10A"    
## [11] "FAU"        "RPL30"      "FOS"        "EEF1A1"     "JUN"       
## [16] "FOSB"       "DNAJA1"     "JUNB"       "AC022217.3" "TUBA1A"    
## [21] "IER2"       "AL606489.1" "IER5"       "DDX3Y"      "SLC38A2"   
## [26] "TEX14"      "IFRD1"      "ID2"       
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
##  [1] "CAMK4"      "LEF1"       "PRKCA"      "SERINC5"    "INPP4B"    
##  [6] "ANK3"       "TSHZ2"      "HIVEP2"     "MAML2"      "CDC14A"    
## [11] "MAP3K1"     "PAG1"       "CSGALNACT1" "GNAQ"       "TTC39C"    
## [16] "PDE3B"      "MGAT5"      "ZEB1"       "PLCL1"      "RASGRF2"   
## [21] "TMEM123"    "FAAH2"      "EPHA4"      "ARHGAP15"   "ZBTB20"    
## [26] "AC139720.1" "PCSK5"      "SAMD12"     "CMTM8"      "AC233976.1"
## [31] "SATB1-AS1" 
## 
## $blue
##  [1] "AOAH"       "ZEB2"       "AC243829.2" "C1orf21"    "TGFBR3"    
##  [6] "PPP2R2B"    "SAMD3"      "ARHGAP26"   "VAV3"       "DTHD1"     
## [11] "LINC02384"  "AL392086.3" "CMIP"       "HIVEP3"     "SYTL2"     
## 
## $brown
##  [1] "RPLP1"      "RPLP2"      "RPL13"      "RPL28"      "RPL41"     
##  [6] "RPS2"       "RPL3"       "RPL13A"     "RPL19"      "RPL10A"    
## [11] "FAU"        "RPL30"      "FOS"        "EEF1A1"     "JUN"       
## [16] "FOSB"       "DNAJA1"     "JUNB"       "AC022217.3" "TUBA1A"    
## [21] "IER2"       "AL606489.1" "IER5"       "DDX3Y"      "SLC38A2"   
## [26] "TEX14"      "IFRD1"      "ID2"       
## 
## [1] "5035_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.7698
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.5018
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.156e-15
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  RPL13, RPLP2, INPP4B, RPL41, RPS12, RPS2, RPL3, RPL13A, JUN, TSHZ2 
##     LEF1, CAMK4, FOSB, FOS, JUNB, SERINC5, PRKCA, FHIT, ANK3, IER2 
## Negative:  ZEB2, C1orf21, AOAH, TGFBR3, GNLY, PPP2R2B, OSBPL5, SYNE1, AC243829.2, NCALD 
##     KLRC3, SETBP1, KLRD1, SGCD, LYN, KLRK1, ADGRG5, VAV3, KLRF1, LINC02384 
## PC_ 2 
## Positive:  C1orf21, RPL13A, ZEB2, GNLY, RPLP2, RPS12, CTBP2, KLRC3, SETBP1, RPL13 
##     KLRK1, RPL41, OSBPL5, AOAH, RPL3, LYN, AC243829.2, PRSS23, EPB41L4A, NCAM1 
## Negative:  INPP4B, PAG1, ARHGAP15, CAMK4, CDC14A, SERINC5, ANK3, MGAT5, THEMIS, RORA 
##     HIVEP2, ZBTB20, PRKCA, NR3C2, MDFIC, TNFAIP8, FMN1, PATJ, FOXP1, CD44 
## PC_ 3 
## Positive:  PVT1, F5, XYLT1, ZMIZ1, ADAM19, AP002383.2, LINC02694, ST8SIA1, AL136456.1, AC006369.1 
##     TOX, MCC, PTPRJ, SLC16A1-AS1, MIB1, Z94721.1, PTPN13, MBOAT1, FBXL18, AC027097.2 
## Negative:  JUN, FOSB, JUNB, IFRD1, FOS, RPL41, DNAJA1, DDX3Y, IER2, NAMPT 
##     RPS12, RPL13A, DUSP1, RPS2, RPL13, RPLP2, EGR1, EIF4A3, SLC2A3, RPL3 
## PC_ 4 
## Positive:  LINC02694, TOX, TTN, ENTPD1, ST8SIA1, IKZF2, LINC01362, SEMA5A, GLCCI1, ATXN1 
##     AC013652.1, RTKN2, CDRT4, LINC02725, ST8SIA6, PAM, LINC00426, NIBAN1, CYTOR, S100Z 
## Negative:  PTPN13, PLCB1, ADAM12, PCSK5, CCR6, PDE4D, BCL2, SASH1, ANK1, GREM2 
##     CR1, AFDN, BACH2, PLXNA4, MB21D2, ABCB1, IGF1R, COL5A3, RBMS1, PELI2 
## PC_ 5 
## Positive:  FRY, LINC02694, PTPN13, ADAM12, PDE4D, COL5A3, AL136456.1, C21orf91-OT1, AUTS2, NIBAN1 
##     LRP12, LINC00299, NEDD4L, NAMPT, STAM, AC013652.1, CCR6, MCF2L2, MSC-AS1, SEMA5A 
## Negative:  IGF1R, AK5, EPHA1-AS1, SORCS3, NELL2, MAML2, LEF1, CERS6, ACTN1, FHIT 
##     UBE2E2, PTPDC1, BCL9, AC233976.1, TSHZ2, SESN3, PRKN, EDAR, MTMR8, MAN1C1 
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.1180 -13.60        0.82900 77.2000  77.20000 80.500
## 2      2   0.0197  -2.59        0.96500 40.2000  40.30000 43.700
## 3      3   0.1540  -4.41        0.95700 21.3000  21.40000 24.900
## 4      4   0.4870  -5.63        0.87200 11.6000  11.70000 15.600
## 5      5   0.6720  -4.72        0.84600  6.4100   6.38000 10.300
## 6      6   0.2240  -8.26        0.00687  3.6500   3.51000  7.150
## 7      7   0.2360  -6.62        0.02380  2.1300   1.98000  5.120
## 8      8   0.2390  -5.56        0.03180  1.2800   1.11000  3.760
## 9      9   0.2400  -4.73        0.03670  0.7920   0.63300  2.810
## 10    10   0.2390  -4.11        0.03920  0.5040   0.36600  2.130
## 11    12   0.2630  -3.54        0.14400  0.2220   0.12500  1.260
## 12    14   0.2500  -3.01        0.11600  0.1080   0.04430  0.767
## 13    16   0.8890  -1.32        0.85800  0.0569   0.01690  0.476
## 14    18   0.8650  -1.19        0.85000  0.0320   0.00625  0.301
## 15    20   0.8090  -1.14        0.79900  0.0189   0.00235  0.201

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  0  1  2  3  4 
## 81 26 16 15 14

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $turquoise
##  [1] "RPL13"   "RPLP2"   "RPL41"   "RPS12"   "RPS2"    "RPL3"    "RPL13A" 
##  [8] "JUN"     "FOSB"    "FOS"     "JUNB"    "IER2"    "DUSP1"   "DNAJA1" 
## [15] "TNFAIP3" "MALAT1"  "IFRD1"   "DDX3Y"   "NAMPT"   "EGR1"    "EIF4A3" 
## [22] "SLC2A3"  "SLC10A1" "RGCC"    "ANXA1"   "TUBA1A" 
## 
## $brown
##  [1] "INPP4B"   "CAMK4"    "SERINC5"  "ANK3"     "PAG1"     "ARHGAP15"
##  [7] "CDC14A"   "MGAT5"    "THEMIS"   "HIVEP2"   "TNFAIP8"  "CD44"    
## [13] "ADAM19"   "TNIK"     "PVT1"    
## 
## $blue
##  [1] "ZEB2"       "C1orf21"    "AOAH"       "TGFBR3"     "GNLY"      
##  [6] "PPP2R2B"    "OSBPL5"     "SYNE1"      "AC243829.2" "NCALD"     
## [11] "KLRC3"      "SETBP1"     "KLRD1"      "SGCD"       "LYN"       
## [16] "KLRK1"      "ADGRG5"     "VAV3"       "KLRF1"      "LINC02384" 
## [21] "CTBP2"      "IKZF2"      "NCAM1"      "PDGFD"      "AC093865.1"
## [26] "PRSS23"     "EPB41L4A"   "CCL5"       "ABCB1"      "MYBL1"     
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
##  [1] "RPL13"   "RPLP2"   "RPL41"   "RPS12"   "RPS2"    "RPL3"    "RPL13A" 
##  [8] "JUN"     "FOSB"    "FOS"     "JUNB"    "IER2"    "DUSP1"   "DNAJA1" 
## [15] "TNFAIP3" "MALAT1"  "IFRD1"   "DDX3Y"   "NAMPT"   "EGR1"    "EIF4A3" 
## [22] "SLC2A3"  "SLC10A1" "RGCC"    "ANXA1"   "TUBA1A" 
## 
## $brown
##  [1] "INPP4B"   "CAMK4"    "SERINC5"  "ANK3"     "PAG1"     "ARHGAP15"
##  [7] "CDC14A"   "MGAT5"    "THEMIS"   "HIVEP2"   "TNFAIP8"  "CD44"    
## [13] "ADAM19"   "TNIK"     "PVT1"    
## 
## $blue
##  [1] "ZEB2"       "C1orf21"    "AOAH"       "TGFBR3"     "GNLY"      
##  [6] "PPP2R2B"    "OSBPL5"     "SYNE1"      "AC243829.2" "NCALD"     
## [11] "KLRC3"      "SETBP1"     "KLRD1"      "SGCD"       "LYN"       
## [16] "KLRK1"      "ADGRG5"     "VAV3"       "KLRF1"      "LINC02384" 
## [21] "CTBP2"      "IKZF2"      "NCAM1"      "PDGFD"      "AC093865.1"
## [26] "PRSS23"     "EPB41L4A"   "CCL5"       "ABCB1"      "MYBL1"     
## 
## [1] "5026_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.8736
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 2.0588e-15

## PC_ 1 
## Positive:  ARHGAP15, RORA, SKAP1, PAG1, SOS1, LINC01619, GPRIN3, DPYD, FRY, RABGAP1L 
##     ADAM19, RUNX2, INPP4B, CHST11, CDC14A, ZBTB20, FOXO1, PPP3CA, PPP1R16B, NIBAN1 
## Negative:  RPL13, RPLP2, RPLP1, RPS18, RPL41, RPS19, RPS23, RPS28, RPS27A, RPS12 
##     RPS2, FOS, JUN, FOSB, IER2, AC022217.3, AL691403.1, AC103591.3, EGR1, EIF4A3 
## PC_ 2 
## Positive:  LINC02694, IKZF2, AC093865.1, TOX, IL2RA, TTN, CCDC141, HPGD, RTKN2, AC013652.1 
##     MIR4435-2HG, CYTOR, DUSP4, STAM, ENTPD1, PALM2-AKAP2, NIBAN1, ST8SIA6, GPR55, RGS1 
## Negative:  ANK3, BACH2, PRKCA, NELL2, RASGRF2, NR3C2, PCSK5, BTBD11, PELI2, RBMS1 
##     UST, PDE4D, PRKN, IGF1R, SBF2, APBA2, EDA, MGAT5, THEMIS, ITGA4 
## PC_ 3 
## Positive:  PDE4D, PLCB1, FRY, ADAM12, LINC00299, LATS2, PTPN13, AL136456.1, ABCB1, NCALD 
##     SYTL2, MYBL1, TNFAIP3, AGAP1, RUNX2, AUTS2, SLC4A10, PPP2R2B, KIF5C, ZEB2 
## Negative:  LEF1, FOXP1, UBASH3B, ARID5B, MAN2A1, ICOS, TSHZ2, MAML2, APBA2, SLC9A9 
##     CMTM8, AC139720.1, SESN3, FAAH2, CERS6, AL353660.1, SLC22A23, FHIT, FKBP5, AC233976.1 
## PC_ 4 
## Positive:  RUNX1, AOAH, UBASH3B, PPP1R16B, LYN, ZFPM1, ZEB2, CMTM8, C1orf21, TSHZ2 
##     ETV6, BTBD11, GRK5, ATXN7L1, PRR5L, DISC1, IFNG-AS1, KIAA1671, ADCY9, SGCD 
## Negative:  FOSB, FOS, RPS2, JUN, RPS28, AC022217.3, RPS19, RPL41, RPS23, RPS12 
##     RPLP1, RPS18, RPL13, DNAJA1, RPLP2, RPS27A, PLCG2, IER2, EIF4A3, TEX14 
## PC_ 5 
## Positive:  AL136456.1, IL2RA, BCL2, IKZF2, HPGD, PLCL1, AC093865.1, LDLRAD4, ADAM12, IGF1R 
##     PTPN13, RTKN2, AL589693.1, CR1, SAMD12, FAM13A, DST, CCDC141, GPR55, ENTPD1 
## Negative:  TGFBR3, ZEB2, PRR5L, SLF1, C1orf21, AOAH, NR3C1, TPRG1, ANXA1, KLRK1 
##     PDGFD, FOSB, EDARADD, SAMD3, ANK3, RAB27B, TBXAS1, PPP1R16B, ARHGAP26, IFNG-AS1 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1  0.00884  -3.74        0.88400 101.0000  1.01e+02 106.000
## 2      2  0.24200 -11.10        0.85700  51.7000  5.14e+01  57.900
## 3      3  0.74500 -15.20        0.86500  26.8000  2.64e+01  32.000
## 4      4  0.63900 -11.20        0.71500  14.0000  1.38e+01  17.900
## 5      5  0.62000  -8.34        0.71600   7.4200  7.23e+00  10.200
## 6      6  0.64900  -4.86        0.83400   3.9800  3.80e+00   5.840
## 7      7  0.70100  -3.82        0.61600   2.1700  2.02e+00   3.690
## 8      8  0.21600  -7.69       -0.00302   1.2100  1.09e+00   2.640
## 9      9  0.67500  -3.04        0.75800   0.6890  5.92e-01   1.990
## 10    10  0.12400  -3.56        0.06370   0.4030  3.22e-01   1.550
## 11    12  0.17700  -3.16        0.02010   0.1530  1.00e-01   0.992
## 12    14  0.08760  -1.75        0.06620   0.0670  3.07e-02   0.659
## 13    16  0.12300  -1.76       -0.00561   0.0337  9.71e-03   0.446
## 14    18  0.61400  -1.01        0.98100   0.0189  3.08e-03   0.304
## 15    20  0.07170  -1.06        0.05750   0.0114  1.03e-03   0.208

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  1  2  3  4  5  6  7  8  9 
## 57 28 24 19 19 15 14 13 10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 7 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 7 module eigengenes in given set.
## $green
##  [1] "ARHGAP15"   "PAG1"       "SOS1"       "LINC01619"  "GPRIN3"    
##  [6] "DPYD"       "ADAM19"     "INPP4B"     "CDC14A"     "ZBTB20"    
## [11] "FOXO1"      "PPP3CA"     "MBNL1"      "MGAT5"      "DOCK10"    
## [16] "ANK3"       "BACH2"      "PRKCA"      "NELL2"      "RASGRF2"   
## [21] "NR3C2"      "UST"        "APBA2"      "EDA"        "THEMIS"    
## [26] "ITGA4"      "GREM2"      "SAMD12"     "LEF1"       "FOXP1"     
## [31] "UBASH3B"    "ARID5B"     "MAN2A1"     "ICOS"       "TSHZ2"     
## [36] "MAML2"      "SLC9A9"     "CMTM8"      "AC139720.1" "SESN3"     
## [41] "FAAH2"      "CERS6"      "AL353660.1" "SLC22A23"   "FHIT"      
## [46] "FKBP5"      "AC233976.1" "PLCL1"      "MLLT3"      "RUNX1"     
## [51] "ZFPM1"      "ETV6"       "PRR5L"      "DISC1"      "IFNG-AS1"  
## [56] "ADCY9"      "GNAO1"      "AL589693.1" "CR1"        "FAM13A"    
## [61] "PLXNA4"     "TPRG1"      "EDARADD"    "SAMD3"      "KIAA0825"  
## [66] "LINC01934"  "LINC02384"  "KCNQ5"      "TIAM1"      "GAB2"      
## [71] "EEPD1"      "CSGALNACT1" "ACVR2A"     "LINC00511"  "CYSLTR1"   
## [76] "TRIM2"     
## 
## $brown
##  [1] "RORA"       "FRY"        "RUNX2"      "TANK"       "IGF1R"     
##  [6] "PCSK5"      "BTBD11"     "PELI2"      "RBMS1"      "PDE4D"     
## [11] "PRKN"       "SBF2"       "SATB1-AS1"  "PLCB1"      "ADAM12"    
## [16] "LINC00299"  "LATS2"      "PTPN13"     "AL136456.1" "ABCB1"     
## [21] "NCALD"      "SYTL2"      "MYBL1"      "AGAP1"      "AUTS2"     
## [26] "SLC4A10"    "PPP2R2B"    "KIF5C"      "MSC-AS1"    "ELOVL4"    
## [31] "BCL2"       "DST"        "ABCA1"      "MCTP2"     
## 
## $pink
##  [1] "SKAP1"    "RABGAP1L" "CHST11"   "PPP1R16B" "KIAA1671" "TGFBR3"  
##  [7] "SLF1"     "NR3C1"    "RAB27B"   "TBXAS1"   "SEMA5A"   "SNED1"   
## [13] "FGF14"   
## 
## $yellow
##  [1] "NIBAN1"     "PDE4B"      "LINC02694"  "IKZF2"      "AC093865.1"
##  [6] "TOX"        "IL2RA"      "TTN"        "CCDC141"    "HPGD"      
## [11] "RTKN2"      "AC013652.1" "DUSP4"      "STAM"       "RGS1"      
## [16] "MIR181A1HG" "GBP5"       "ATXN7L1"    "LDLRAD4"   
## 
## $black
##  [1] "RPL13"      "RPLP2"      "RPLP1"      "RPS18"      "RPL41"     
##  [6] "RPS19"      "RPS23"      "RPS28"      "RPS27A"     "RPS12"     
## [11] "RPS2"       "AC103591.3" "SH3RF3"     "PLCG2"     
## 
## $red
##  [1] "FOS"        "JUN"        "FOSB"       "IER2"       "AC022217.3"
##  [6] "AL691403.1" "EGR1"       "EIF4A3"     "TEX14"      "CSKMT"     
## [11] "DNAJA1"     "TNFAIP3"    "ID2"        "ANXA1"      "AL360012.1"
## 
## $blue
##  [1] "MIR4435-2HG" "CYTOR"       "ENTPD1"      "PALM2-AKAP2" "ST8SIA6"    
##  [6] "GPR55"       "MYB"         "BARD1"       "CENPE"       "ZEB2"       
## [11] "GRK5"        "SLC16A10"    "AOAH"        "LYN"         "C1orf21"    
## [16] "SGCD"        "PDGFD"       "SETBP1"      "KLRK1"       "ARHGAP26"   
## [21] "GNLY"        "VAV3"        "ADGRG1"      "CTBP2"       "SLC4A4"     
## [26] "TMCC3"       "DAPK2"       "ITGAX"      
## 
## [1] "128/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "751/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "101/10000 permutations failed the Mann-Whitney test."
## $green
##  [1] "ARHGAP15"   "PAG1"       "SOS1"       "LINC01619"  "GPRIN3"    
##  [6] "DPYD"       "ADAM19"     "INPP4B"     "CDC14A"     "ZBTB20"    
## [11] "FOXO1"      "PPP3CA"     "MBNL1"      "MGAT5"      "DOCK10"    
## [16] "ANK3"       "BACH2"      "PRKCA"      "NELL2"      "RASGRF2"   
## [21] "NR3C2"      "UST"        "APBA2"      "EDA"        "THEMIS"    
## [26] "ITGA4"      "GREM2"      "SAMD12"     "LEF1"       "FOXP1"     
## [31] "UBASH3B"    "ARID5B"     "MAN2A1"     "ICOS"       "TSHZ2"     
## [36] "MAML2"      "SLC9A9"     "CMTM8"      "AC139720.1" "SESN3"     
## [41] "FAAH2"      "CERS6"      "AL353660.1" "SLC22A23"   "FHIT"      
## [46] "FKBP5"      "AC233976.1" "PLCL1"      "MLLT3"      "RUNX1"     
## [51] "ZFPM1"      "ETV6"       "PRR5L"      "DISC1"      "IFNG-AS1"  
## [56] "ADCY9"      "GNAO1"      "AL589693.1" "CR1"        "FAM13A"    
## [61] "PLXNA4"     "TPRG1"      "EDARADD"    "SAMD3"      "KIAA0825"  
## [66] "LINC01934"  "LINC02384"  "KCNQ5"      "TIAM1"      "GAB2"      
## [71] "EEPD1"      "CSGALNACT1" "ACVR2A"     "LINC00511"  "CYSLTR1"   
## [76] "TRIM2"     
## 
## $brown
##  [1] "RORA"       "FRY"        "RUNX2"      "TANK"       "IGF1R"     
##  [6] "PCSK5"      "BTBD11"     "PELI2"      "RBMS1"      "PDE4D"     
## [11] "PRKN"       "SBF2"       "SATB1-AS1"  "PLCB1"      "ADAM12"    
## [16] "LINC00299"  "LATS2"      "PTPN13"     "AL136456.1" "ABCB1"     
## [21] "NCALD"      "SYTL2"      "MYBL1"      "AGAP1"      "AUTS2"     
## [26] "SLC4A10"    "PPP2R2B"    "KIF5C"      "MSC-AS1"    "ELOVL4"    
## [31] "BCL2"       "DST"        "ABCA1"      "MCTP2"     
## 
## $yellow
##  [1] "NIBAN1"     "PDE4B"      "LINC02694"  "IKZF2"      "AC093865.1"
##  [6] "TOX"        "IL2RA"      "TTN"        "CCDC141"    "HPGD"      
## [11] "RTKN2"      "AC013652.1" "DUSP4"      "STAM"       "RGS1"      
## [16] "MIR181A1HG" "GBP5"       "ATXN7L1"    "LDLRAD4"   
## 
## $black
##  [1] "RPL13"      "RPLP2"      "RPLP1"      "RPS18"      "RPL41"     
##  [6] "RPS19"      "RPS23"      "RPS28"      "RPS27A"     "RPS12"     
## [11] "RPS2"       "AC103591.3" "SH3RF3"     "PLCG2"     
## 
## $red
##  [1] "FOS"        "JUN"        "FOSB"       "IER2"       "AC022217.3"
##  [6] "AL691403.1" "EGR1"       "EIF4A3"     "TEX14"      "CSKMT"     
## [11] "DNAJA1"     "TNFAIP3"    "ID2"        "ANXA1"      "AL360012.1"
## 
## $blue
##  [1] "MIR4435-2HG" "CYTOR"       "ENTPD1"      "PALM2-AKAP2" "ST8SIA6"    
##  [6] "GPR55"       "MYB"         "BARD1"       "CENPE"       "ZEB2"       
## [11] "GRK5"        "SLC16A10"    "AOAH"        "LYN"         "C1orf21"    
## [16] "SGCD"        "PDGFD"       "SETBP1"      "KLRK1"       "ARHGAP26"   
## [21] "GNLY"        "VAV3"        "ADGRG1"      "CTBP2"       "SLC4A4"     
## [26] "TMCC3"       "DAPK2"       "ITGAX"      
## 
## [1] "5026_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.5932
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50095
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 8.4361e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  ARHGAP15, RORA, DPYD, MBNL1, NEK7, CDC14A, PAM, SAMSN1, BBS9, NR3C1 
##     PPP3CA, RNF19A, ZFAND6, TANK, MDFIC, CBLB, FTO, FRY, RBMS1, CNOT6L 
## Negative:  RPL13A, RPL38, RPL13, RPL28, RPLP2, RPLP1, RPS18, RPS23, EEF1A1, RPS11 
##     RPS19, RPS12, RPL37, RPS28, RPL23A, RPL41, RPL37A, RPS2, JUN, FOSB 
## PC_ 2 
## Positive:  LINC02694, IKZF2, TTN, RTKN2, IL2RA, AC093865.1, CCDC141, TOX, CDHR3, STAM 
##     HPGD, AC013652.1, ST8SIA6, ENTPD1, PALM2-AKAP2, MIR4435-2HG, CYTOR, RBBP8, ATXN7L1, JAZF1 
## Negative:  ANK3, BACH2, PRKCA, NELL2, NR3C2, RASGRF2, RBMS1, PDE4D, THEMIS, INPP4B 
##     FRY, PABPC1, BTBD11, FKBP5, PLCB1, STAT4, UST, PELI2, PCSK5, EDA 
## PC_ 3 
## Positive:  DUSP1, RPS2, JUN, FOSB, DNAJA1, FOS, RPS28, RPL13, RPL41, RPS23 
##     RPL28, RPS19, RPLP1, LTB, RPLP2, JUNB, RPS18, RPS12, EEF1A1, NEU1 
## Negative:  BTBD11, SLCO3A1, ADAM19, ADAM12, FRY, MYBL1, GRAP2, PTPN13, STX18-AS1, GALNT10 
##     PIN4, SIDT1, PPP1R16B, AL136962.1, LINC00299, PPP2R2B, LINC02649, PLCB1, GRAMD1B, BCL2 
## PC_ 4 
## Positive:  C1orf21, ZEB2, FAM49A, AOAH, DOCK5, SAMD3, KLRF1, AGAP1, SYTL2, KLRK1 
##     OSBPL5, SPON2, LINC02384, CD8B, SGCD, TRIO, KIAA1671, DTHD1, MCTP2, PLCB1 
## Negative:  TSHZ2, INPP4B, PLCL1, ARID5B, SESN3, CMTM8, ICOS, ACVR2A, GCNT4, AL353660.1 
##     TTC39B, CYSLTR1, FMN1, PRKCA, LINC01550, MAN1C1, TIAM1, CSGALNACT1, AC139720.1, SELL 
## PC_ 5 
## Positive:  AOAH, C1orf21, KLRK1, FAM49A, ZEB2, SPON2, SGCD, KLRF1, KIAA1671, TPRG1 
##     OSBPL5, UTY, SLF1, DOCK5, MTSS1, USP9Y, KDM5D, SNTB1, GNAO1, AC243829.2 
## Negative:  AL136456.1, ADAM12, PDE4D, CCR6, BCL2, PTPN13, EDA, MAP3K4, LINC00299, RORA 
##     MB21D2, IL2RA, LDLRAD4, FRY, DUSP16, PLCB1, ARHGEF7, MAN1A1, SLC4A10, TNFRSF11A 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1 0.014300 -5.950          0.905 130.0000  1.30e+02 135.000
## 2      2 0.005390  1.580          0.813  66.9000  6.66e+01  72.500
## 3      3 0.000218 -0.191          0.795  34.9000  3.46e+01  39.800
## 4      4 0.069100 -2.330          0.859  18.4000  1.82e+01  22.900
## 5      5 0.215000 -2.940          0.855   9.8900  9.66e+00  13.700
## 6      6 0.397000 -3.060          0.708   5.4100  5.15e+00   8.670
## 7      7 0.646000 -2.980          0.796   3.0200  2.79e+00   5.740
## 8      8 0.845000 -2.740          0.890   1.7300  1.52e+00   3.980
## 9      9 0.931000 -2.460          0.936   1.0200  8.40e-01   2.870
## 10    10 0.925000 -2.210          0.908   0.6200  4.71e-01   2.140
## 11    12 0.914000 -1.830          0.896   0.2520  1.49e-01   1.270
## 12    14 0.922000 -1.520          0.905   0.1160  4.90e-02   0.796
## 13    16 0.940000 -1.350          0.928   0.0599  1.67e-02   0.516
## 14    18 0.981000 -1.200          0.977   0.0334  5.91e-03   0.344
## 15    20 0.957000 -1.220          0.968   0.0198  2.16e-03   0.259

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4 
## 195  17  17  14  13

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $blue
##  [1] "RPL13A"     "RPL38"      "RPL13"      "RPL28"      "RPLP2"     
##  [6] "RPLP1"      "RPS18"      "RPS23"      "EEF1A1"     "RPS11"     
## [11] "RPS19"      "RPS12"      "RPL37"      "RPS28"      "RPL23A"    
## [16] "RPL41"      "RPL37A"     "RPS2"       "JUN"        "FOSB"      
## [21] "LTB"        "FOS"        "JUNB"       "ERCC1"      "IER2"      
## [26] "DUSP1"      "DNAJA1"     "NEU1"       "AC022217.3" "IFRD1"     
## [31] "GALM"      
## 
## $yellow
##  [1] "IKZF2"      "TTN"        "RTKN2"      "IL2RA"      "AC093865.1"
##  [6] "CCDC141"    "TOX"        "CDHR3"      "STAM"       "HPGD"      
## [11] "ST8SIA6"    "ATXN7L1"    "JAZF1"     
## 
## $turquoise
##  [1] "STIL"       "KNL1"       "ECT2"       "TOP2A"      "PCLAF"     
##  [6] "CCNF"       "RECQL4"     "RAD51"      "WDR62"      "SPC24"     
## [11] "KIF18B"     "TYMS"       "MND1"       "AC000065.1" "ESCO2"     
## [16] "BRCA2"      "ANLN"      
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
##  [1] "RPL13A"     "RPL38"      "RPL13"      "RPL28"      "RPLP2"     
##  [6] "RPLP1"      "RPS18"      "RPS23"      "EEF1A1"     "RPS11"     
## [11] "RPS19"      "RPS12"      "RPL37"      "RPS28"      "RPL23A"    
## [16] "RPL41"      "RPL37A"     "RPS2"       "JUN"        "FOSB"      
## [21] "LTB"        "FOS"        "JUNB"       "ERCC1"      "IER2"      
## [26] "DUSP1"      "DNAJA1"     "NEU1"       "AC022217.3" "IFRD1"     
## [31] "GALM"      
## 
## $yellow
##  [1] "IKZF2"      "TTN"        "RTKN2"      "IL2RA"      "AC093865.1"
##  [6] "CCDC141"    "TOX"        "CDHR3"      "STAM"       "HPGD"      
## [11] "ST8SIA6"    "ATXN7L1"    "JAZF1"     
## 
## $turquoise
##  [1] "STIL"       "KNL1"       "ECT2"       "TOP2A"      "PCLAF"     
##  [6] "CCNF"       "RECQL4"     "RAD51"      "WDR62"      "SPC24"     
## [11] "KIF18B"     "TYMS"       "MND1"       "AC000065.1" "ESCO2"     
## [16] "BRCA2"      "ANLN"      
## 
## [1] "5020_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.646
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50091
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 3.2953e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  KLF12, ARHGAP15, MBNL1, LINC01619, USP15, ZBTB20, PAG1, IQGAP2, SLC38A1, EXOC4 
##     DPYD, CBLB, FBXW7, ITGB1, RAP1GDS1, RORA, CAMK4, MAN1A2, FYN, FOXP1 
## Negative:  RPS27, RPL19, SEMA3A, PLXNA4, TEX9, ST6GALNAC3, NUP210L, AC022217.3, JUN, PIK3AP1 
##     ABCG2, PLAC8L1, MOB3B, H2AFJ, SGCD, TTC8, SLC2A1-AS1, SETBP1, HIST1H4C, AOAH 
## PC_ 2 
## Positive:  ANK3, BACH2, PRKCA, NELL2, NR3C2, RBMS1, PELI2, PCSK5, UST, THEMIS 
##     RASGRF2, INPP4B, EDA, PRKN, IGF1R, PDE4D, BCL2, MYBL1, ZNF516, ARHGAP15 
## Negative:  LINC02694, TTN, IKZF2, TOX, RTKN2, CCDC141, ST8SIA6, AC093865.1, MIR4435-2HG, STAM 
##     CDHR3, IL2RA, ATXN7L1, CTLA4, ENTPD1, IL7, F5, HPGD, SLC16A10, GBP5 
## PC_ 3 
## Positive:  FHIT, TSHZ2, INPP4B, GNAQ, TXK, SESN3, UBASH3B, AC139720.1, CMTM8, RPL19 
##     IKZF2, FOS, AL353660.1, PRKCA, FOXP1, PLCL1, RTKN2, CERS6, MALAT1, STAM 
## Negative:  C1orf21, ZEB2, GNLY, MVB12B, KLRK1, TGFBR3, IL18RAP, CMIP, MYBL1, AOAH 
##     SYTL3, SETBP1, DTHD1, PLCB1, NCALD, PPP2R2B, AUTS2, SYTL2, MSC-AS1, MAP3K8 
## PC_ 4 
## Positive:  FOSB, JUN, AL691403.1, FOS, LINC00910, NEU1, IER2, ERCC1, DNAJA1, AC022217.3 
##     EGR1, AL499604.1, TUBA1A, AL360012.1, CSKMT, ARF4, DDX3X, AC253572.2, TEX14, IFRD1 
## Negative:  SATB1-AS1, TSHZ2, ARFIP1, AC233976.1, ARID5B, PLXNA4, PRKCB, USP6NL, AL589693.1, PRKCA 
##     RASSF6, FAAH2, AL122035.1, AHCYL2, AC244131.2, LINC01284, DDX60, TSPOAP1-AS1, AKAP6, AC064834.1 
## PC_ 5 
## Positive:  AL136456.1, FRY, MCF2L2, RUNX2, LINC00299, PTPN13, MB21D2, ADAM12, CCR6, KAT2B 
##     AFDN, NTN4, RBMS1, PLD1, MSC-AS1, VCL, WDFY2, HLF, AC010754.1, RORA 
## Negative:  AOAH, C1orf21, ZEB2, DTHD1, KLRK1, RAB27B, PDGFD, GFOD1, KCNQ5, AC243829.2 
##     CD8B, MAP3K8, CBLB, SETBP1, ARID5B, AF165147.1, FYN, A2M-AS1, SAMD3, LINC01934 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.   max.k.
## 1      1    0.223 -11.20          0.624 1.08e+02  1.08e+02 115.0000
## 2      2    0.264  -6.30          0.721 5.61e+01  5.57e+01  63.9000
## 3      3    0.351  -4.94          0.784 2.94e+01  2.90e+01  35.9000
## 4      4    0.381  -4.13          0.815 1.55e+01  1.53e+01  20.4000
## 5      5    0.433  -3.65          0.881 8.25e+00  8.14e+00  11.7000
## 6      6    0.478  -3.43          0.901 4.44e+00  4.36e+00   6.8200
## 7      7    0.504  -2.65          0.932 2.42e+00  2.37e+00   4.0200
## 8      8    0.557  -2.85          0.800 1.33e+00  1.29e+00   2.5100
## 9      9    0.275  -7.00          0.180 7.43e-01  7.22e-01   1.7100
## 10    10    0.320  -6.40          0.220 4.20e-01  4.01e-01   1.2000
## 11    12    0.368  -5.28          0.247 1.41e-01  1.27e-01   0.6450
## 12    14    0.355  -5.50          0.182 5.04e-02  4.08e-02   0.3730
## 13    16    0.388  -4.98          0.251 1.94e-02  1.37e-02   0.2270
## 14    18    0.358  -4.85          0.180 8.09e-03  4.93e-03   0.1420
## 15    20    0.358  -4.29          0.187 3.64e-03  1.73e-03   0.0907

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3 
## 177  13  11  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $blue
##  [1] "KLF12"    "ARHGAP15" "MBNL1"    "ZBTB20"   "PAG1"     "EXOC4"   
##  [7] "DPYD"     "FBXW7"    "CAMK4"    "FTX"      "GNAQ"    
## 
## $turquoise
##  [1] "JUN"        "FOS"        "FOSB"       "AL691403.1" "LINC00910" 
##  [6] "NEU1"       "IER2"       "ERCC1"      "DNAJA1"     "EGR1"      
## [11] "TUBA1A"     "IFRD1"      "ATP2B1-AS1"
## 
## $brown
##  [1] "TTN"         "IKZF2"       "TOX"         "CCDC141"     "ST8SIA6"    
##  [6] "AC093865.1"  "MIR4435-2HG" "CDHR3"       "IL2RA"       "SLC16A10"   
## 
## [1] "42/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
##  [1] "KLF12"    "ARHGAP15" "MBNL1"    "ZBTB20"   "PAG1"     "EXOC4"   
##  [7] "DPYD"     "FBXW7"    "CAMK4"    "FTX"      "GNAQ"    
## 
## $turquoise
##  [1] "JUN"        "FOS"        "FOSB"       "AL691403.1" "LINC00910" 
##  [6] "NEU1"       "IER2"       "ERCC1"      "DNAJA1"     "EGR1"      
## [11] "TUBA1A"     "IFRD1"      "ATP2B1-AS1"
## 
## $brown
##  [1] "TTN"         "IKZF2"       "TOX"         "CCDC141"     "ST8SIA6"    
##  [6] "AC093865.1"  "MIR4435-2HG" "CDHR3"       "IL2RA"       "SLC16A10"   
## 
## [1] "5016_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.6483
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50116
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 9.7084e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  INPP4B, MGAT5, ANK3, PRKCA, CDC14A, ARHGAP15, FOXP1, MAP3K1, PAG1, GNAQ 
##     MAML2, NR3C2, FKBP5, CSGALNACT1, TSHZ2, CASK, GPHN, ETV6, DUSP16, ADAM19 
## Negative:  AOAH, ZEB2, AC243829.2, C1orf21, SETBP1, GNLY, KLRD1, SYNE1, NCAM1, OSBPL5 
##     SGCD, PDGFD, VAV3, SAMD3, KLRK1, LYN, LINC02384, ARHGAP26, DTHD1, AL392086.3 
## PC_ 2 
## Positive:  PPP2R2B, RABGAP1L, CHST11, ST6GAL1, GNG2, SAMD3, SYNE1, ATXN1, PTK2B, OSBPL3 
##     AC243829.2, RORA, LPP, LINC02384, JAZF1, RAB27A, LINC01619, ARHGAP26, SUSD1, ZEB2 
## Negative:  RPL13, RPLP2, RPS2, RPL41, RPS16, RPS27, JUN, FOS, JUNB, FOSB 
##     CRIP1, TRBC2, AC022217.3, UBE2E2, ADAMTS17, AC087286.2, PTK2, PARD3B, KANK1, ANXA1 
## PC_ 3 
## Positive:  LINC02694, AC013652.1, RTKN2, IKZF2, STAM, EZH2, JUN, HPGD, TTN, AC022217.3 
##     NAMPT, FOSB, MIR181A1HG, FOS, ATP2B1-AS1, AC093865.1, CCDC141, IER2, CDHR3, ENTPD1 
## Negative:  ANK3, ITGA4, BTBD11, NR3C2, PRKCB, BACH2, PELI2, NELL2, TRABD2A, PCSK5 
##     MAML2, PRKN, ARHGAP5, THEMIS, FKBP5, MCTP2, WNT7A, SNTB1, UST, PLCB1 
## PC_ 4 
## Positive:  PFKFB3, ADAM19, BRCA2, FRY, MKI67, ADAM12, PTPN13, WWC2, COL5A3, RUNX2 
##     ATAD5, BTBD11, E2F7, CEP112, IL2RA, ANK1, CR1, NCAPG2, SLCO3A1, CDC45 
## Negative:  RPS2, RPLP2, RPL41, RPS16, RPS27, FOSB, RPL13, JUN, FOS, JUNB 
##     AC022217.3, DNAJA1, ZNF407, TUBA1A, IFRD1, PZP, TRBC2, ANXA1, TTTY14, ZNF451-AS1 
## PC_ 5 
## Positive:  LRRIQ3, MKI67, CDC45, E2F7, DIAPH3, BRCA2, ASPM, BRIP1, MELK, SMC2 
##     BRCA1, CENPU, ADAM28, AC005400.1, ILDR2, ECT2, NCAPG2, RCAN2, DMPK, GAS2L3 
## Negative:  LINC02694, HPGD, MIR4435-2HG, AC013652.1, CTLA4, TTN, ST6GAL1, BCL2L11, RTKN2, RUNX2 
##     CDHR3, AC011997.1, CCDC141, COMMD1, MIR181A1HG, TNFRSF11A, ZNF365, MECR, ENTPD1, TGFBR3 
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1    0.131 -12.80          0.669 94.3000  94.30000 98.600
## 2      2    0.276 -11.00          0.801 48.8000  48.80000 54.500
## 3      3    0.483  -8.46          0.825 25.6000  25.50000 31.700
## 4      4    0.272 -17.60          0.133 13.7000  13.50000 19.600
## 5      5    0.292 -12.30          0.153  7.4800   7.21000 12.900
## 6      6    0.320  -9.46          0.185  4.1800   3.91000  9.010
## 7      7    0.376 -10.50          0.223  2.3900   2.14000  6.670
## 8      8    0.385  -8.62          0.245  1.4100   1.17000  5.160
## 9      9    0.415  -8.70          0.258  0.8600   0.65000  4.140
## 10    10    0.410  -7.41          0.266  0.5420   0.36900  3.400
## 11    12    0.398  -5.80          0.278  0.2390   0.12300  2.410
## 12    14    0.412  -5.55          0.266  0.1200   0.04280  1.790
## 13    16    0.398  -4.91          0.263  0.0674   0.01520  1.360
## 14    18    0.394  -4.49          0.265  0.0412   0.00572  1.050
## 15    20    0.411  -4.38          0.248  0.0267   0.00219  0.825

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  1  2  3  4  5 
## 63 46 38 28 11

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
## $yellow
##  [1] "INPP4B"   "MGAT5"    "ANK3"     "PRKCA"    "CDC14A"   "ARHGAP15"
##  [7] "FOXP1"    "MAP3K1"   "PAG1"     "GNAQ"     "MAML2"    "TSHZ2"   
## [13] "CASK"     "GPHN"     "DUSP16"   "BACH2"    "IMMP2L"   "RORA"    
## [19] "PARD3B"   "KANK1"    "NELL2"    "TRABD2A"  "PCSK5"    "PRKN"    
## [25] "ARHGAP5"  "WNT7A"    "PLXNA4"   "CEP112"  
## 
## $blue
##  [1] "NR3C2"      "FKBP5"      "CSGALNACT1" "ETV6"       "ADAM19"    
##  [6] "RUNX2"      "ZBTB20"     "LPP"        "LINC01619"  "PARP8"     
## [11] "EZH2"       "ASPM"       "ITGA4"      "BTBD11"     "THEMIS"    
## [16] "LINC01934"  "ZNF609"     "PFKFB3"     "BRCA2"      "FRY"       
## [21] "MKI67"      "PTPN13"     "E2F7"       "NCAPG2"     "SLCO3A1"   
## [26] "CDC45"      "AL589693.1" "CCR6"       "MELK"       "ZNF407"    
## [31] "LRRIQ3"     "DIAPH3"     "BRIP1"      "SMC2"       "BRCA1"     
## [36] "CENPU"      "ADAM28"     "AC005400.1" "ECT2"       "RCAN2"     
## [41] "DMPK"       "GAS2L3"     "PODXL"      "ZGRF1"      "ESCO2"     
## [46] "TOP2A"     
## 
## $turquoise
##  [1] "AOAH"       "ZEB2"       "AC243829.2" "C1orf21"    "SETBP1"    
##  [6] "GNLY"       "KLRD1"      "SYNE1"      "NCAM1"      "OSBPL5"    
## [11] "SGCD"       "PDGFD"      "VAV3"       "SAMD3"      "KLRK1"     
## [16] "LYN"        "LINC02384"  "ARHGAP26"   "DTHD1"      "AL392086.3"
## [21] "LGR6"       "TGFBR3"     "LRFN2"      "KLRF1"      "ADGRG5"    
## [26] "PPP2R2B"    "GNG2"       "ATXN1"      "JAZF1"      "SYTL2"     
## [31] "SGMS1"      "LINC02694"  "AC013652.1" "RTKN2"      "IKZF2"     
## [36] "STAM"       "HPGD"       "TTN"        "MIR181A1HG" "AC093865.1"
## [41] "CCDC141"    "CDHR3"      "ENTPD1"     "IL2RA"      "MCTP2"     
## [46] "SNTB1"      "PLCB1"      "ADAM12"     "WWC2"       "COL5A3"    
## [51] "ANK1"       "CR1"        "ZMIZ1"      "PZP"        "KCNQ5"     
## [56] "CTLA4"      "AC011997.1" "COMMD1"     "TNFRSF11A"  "ZNF365"    
## [61] "CSF2RB"     "LINC00426"  "AL096794.1"
## 
## $green
##  [1] "RABGAP1L"    "CHST11"      "ST6GAL1"     "PTK2B"       "OSBPL3"     
##  [6] "RAB27A"      "SUSD1"       "PRKCB"       "MIR4435-2HG" "BCL2L11"    
## [11] "MECR"       
## 
## $brown
##  [1] "RPL13"      "RPLP2"      "RPS2"       "RPL41"      "RPS16"     
##  [6] "RPS27"      "JUN"        "FOS"        "JUNB"       "FOSB"      
## [11] "CRIP1"      "TRBC2"      "AC022217.3" "UBE2E2"     "ADAMTS17"  
## [16] "AC087286.2" "PTK2"       "ANXA1"      "DNAJA1"     "TUBA1A"    
## [21] "ATP8B1"     "ATP2B1-AS1" "NAMPT"      "IER2"       "LMNA"      
## [26] "RGS1"       "PELI2"      "UST"        "ZNF516"     "TAFA1"     
## [31] "ATAD5"      "STIMATE"    "IFRD1"      "TTTY14"     "ZNF451-AS1"
## [36] "TNFAIP3"    "YPEL5"      "ILDR2"     
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "3/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1233/10000 permutations failed the Mann-Whitney test."
## [1] "19/10000 permutations failed the Mann-Whitney test."
## $yellow
##  [1] "INPP4B"   "MGAT5"    "ANK3"     "PRKCA"    "CDC14A"   "ARHGAP15"
##  [7] "FOXP1"    "MAP3K1"   "PAG1"     "GNAQ"     "MAML2"    "TSHZ2"   
## [13] "CASK"     "GPHN"     "DUSP16"   "BACH2"    "IMMP2L"   "RORA"    
## [19] "PARD3B"   "KANK1"    "NELL2"    "TRABD2A"  "PCSK5"    "PRKN"    
## [25] "ARHGAP5"  "WNT7A"    "PLXNA4"   "CEP112"  
## 
## $blue
##  [1] "NR3C2"      "FKBP5"      "CSGALNACT1" "ETV6"       "ADAM19"    
##  [6] "RUNX2"      "ZBTB20"     "LPP"        "LINC01619"  "PARP8"     
## [11] "EZH2"       "ASPM"       "ITGA4"      "BTBD11"     "THEMIS"    
## [16] "LINC01934"  "ZNF609"     "PFKFB3"     "BRCA2"      "FRY"       
## [21] "MKI67"      "PTPN13"     "E2F7"       "NCAPG2"     "SLCO3A1"   
## [26] "CDC45"      "AL589693.1" "CCR6"       "MELK"       "ZNF407"    
## [31] "LRRIQ3"     "DIAPH3"     "BRIP1"      "SMC2"       "BRCA1"     
## [36] "CENPU"      "ADAM28"     "AC005400.1" "ECT2"       "RCAN2"     
## [41] "DMPK"       "GAS2L3"     "PODXL"      "ZGRF1"      "ESCO2"     
## [46] "TOP2A"     
## 
## $turquoise
##  [1] "AOAH"       "ZEB2"       "AC243829.2" "C1orf21"    "SETBP1"    
##  [6] "GNLY"       "KLRD1"      "SYNE1"      "NCAM1"      "OSBPL5"    
## [11] "SGCD"       "PDGFD"      "VAV3"       "SAMD3"      "KLRK1"     
## [16] "LYN"        "LINC02384"  "ARHGAP26"   "DTHD1"      "AL392086.3"
## [21] "LGR6"       "TGFBR3"     "LRFN2"      "KLRF1"      "ADGRG5"    
## [26] "PPP2R2B"    "GNG2"       "ATXN1"      "JAZF1"      "SYTL2"     
## [31] "SGMS1"      "LINC02694"  "AC013652.1" "RTKN2"      "IKZF2"     
## [36] "STAM"       "HPGD"       "TTN"        "MIR181A1HG" "AC093865.1"
## [41] "CCDC141"    "CDHR3"      "ENTPD1"     "IL2RA"      "MCTP2"     
## [46] "SNTB1"      "PLCB1"      "ADAM12"     "WWC2"       "COL5A3"    
## [51] "ANK1"       "CR1"        "ZMIZ1"      "PZP"        "KCNQ5"     
## [56] "CTLA4"      "AC011997.1" "COMMD1"     "TNFRSF11A"  "ZNF365"    
## [61] "CSF2RB"     "LINC00426"  "AL096794.1"
## 
## $brown
##  [1] "RPL13"      "RPLP2"      "RPS2"       "RPL41"      "RPS16"     
##  [6] "RPS27"      "JUN"        "FOS"        "JUNB"       "FOSB"      
## [11] "CRIP1"      "TRBC2"      "AC022217.3" "UBE2E2"     "ADAMTS17"  
## [16] "AC087286.2" "PTK2"       "ANXA1"      "DNAJA1"     "TUBA1A"    
## [21] "ATP8B1"     "ATP2B1-AS1" "NAMPT"      "IER2"       "LMNA"      
## [26] "RGS1"       "PELI2"      "UST"        "ZNF516"     "TAFA1"     
## [31] "ATAD5"      "STIMATE"    "IFRD1"      "TTTY14"     "ZNF451-AS1"
## [36] "TNFAIP3"    "YPEL5"      "ILDR2"     
## 
## [1] "5035_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.8223
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.50218
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 8.3085e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  ZEB2, AOAH, C1orf21, GNLY, OSBPL5, LYN, KLRD1, PDGFD, SGCD, TGFBR3 
##     KLRC3, IKZF2, CTBP2, SETBP1, AC243829.2, TPST2, AGAP1, AC093865.1, MCTP2, NCAM1 
## Negative:  INPP4B, PAG1, CAMK4, ANK3, CDC14A, ARHGAP15, PRKCA, LEF1, ADAM19, BCL2 
##     TTC39C, MGAT5, MAP3K1, MDFIC, HIVEP2, GNAQ, NR3C2, FOXP1, DOCK10, AC139720.1 
## PC_ 2 
## Positive:  PARP8, MCTP2, CBLB, MYBL1, TGFBR3, C1orf21, KLF12, RORA, SAMD3, NCALD 
##     ZEB2, PCNX1, CHST11, ARHGAP26, JAZF1, PPP3CA, ABCB1, AOAH, SYTL2, PPP2R2B 
## Negative:  RPL13, RPLP2, RPL34, RPL28, RPL13A, RPS19, TMSB10, RPL41, RPL38, RPS28 
##     JUN, RPL3, RPLP1, RPS18, FOS, RPS8, RPS2, RPS12, RPL18A, FOSB 
## PC_ 3 
## Positive:  JUN, FOSB, FOS, JUNB, IER2, AC079793.1, AC022217.3, RPS2, TUBA1A, RPLP1 
##     RPL41, TEX14, RPS12, NAMPT, RPL3, EGR1, RPLP2, RPL13, IFRD1, RPL18A 
## Negative:  ADAM19, PAG1, MFHAS1, CHST11, GRAMD1B, ADAMTS17, ERN1, TIAM1, ZMIZ1-AS1, KANK1 
##     LINC02649, SASH1, ATXN7L1, UBASH3B, PACSIN2, ATF7IP2, EGLN3, FRY, LINC01550, CLIC5 
## PC_ 4 
## Positive:  PLCB1, BTBD11, BACH2, IGF1R, MYBL1, ITGA4, PELI2, DPP4, GREM2, RASGRF2 
##     PDE4D, PCSK5, ADAM23, NELL2, ALOX5, ZNF516, TXK, MCTP2, RNF157, BCL2 
## Negative:  LINC02694, TTN, TOX, SNED1, CCDC141, CDHR3, RTKN2, AC013652.1, ENTPD1, STAM 
##     DLEU2, SEMA5A, F5, SPSB1, CYTOR, LINC01362, ST8SIA4, ZC2HC1A, CD109, MIR4435-2HG 
## PC_ 5 
## Positive:  ST8SIA1, IFNG-AS1, MAN2A1, SESN3, UBASH3B, AL353660.1, ARID5B, FHIT, TXK, CERS6 
##     FOXP1, LEF1, SNTB1, MAML2, LINC01934, NELL2, AC139720.1, DOCK10, LINC01550, DISC1 
## Negative:  FRY, PTPN13, AL136456.1, COL5A3, MCF2L2, MSC-AS1, SASH1, PDE4D, LINC00299, RUNX2 
##     IL1R1, ADAM12, LINC01644, CCR6, NEDD4L, NCAPG2, ALOX5, KAT2B, B4GALT5, LINC02694 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1    0.277 -24.70        0.84000 112.0000  1.11e+02 119.000
## 2      2    0.402 -14.10        0.76500  57.9000  5.75e+01  66.200
## 3      3    0.385  -8.30        0.81800  30.6000  3.04e+01  37.800
## 4      4    0.410  -5.53        0.79400  16.4000  1.63e+01  22.100
## 5      5    0.549  -4.07        0.88200   9.0000  8.95e+00  13.100
## 6      6    0.599  -3.12        0.78400   5.0300  4.87e+00   8.160
## 7      7    0.745  -3.32        0.87400   2.8700  2.70e+00   5.660
## 8      8    0.889  -3.06        0.96800   1.6700  1.50e+00   4.050
## 9      9    0.905  -2.74        0.94000   1.0000  8.52e-01   2.970
## 10    10    0.897  -2.55        0.90300   0.6130  4.89e-01   2.210
## 11    12    0.828  -2.19        0.78000   0.2470  1.63e-01   1.290
## 12    14    0.302  -3.42        0.17900   0.1100  5.67e-02   0.851
## 13    16    0.229  -2.59        0.00927   0.0531  1.99e-02   0.606
## 14    18    0.199  -3.29       -0.01260   0.0279  7.24e-03   0.447
## 15    20    0.327  -3.49        0.21600   0.0157  2.62e-03   0.339

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5 
## 127  30  22  14  14  12

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 6 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $blue
##  [1] "ZEB2"        "AOAH"        "C1orf21"     "GNLY"        "OSBPL5"     
##  [6] "LYN"         "SGCD"        "TGFBR3"      "KLRC3"       "IKZF2"      
## [11] "SETBP1"      "TPST2"       "AGAP1"       "AC093865.1"  "NCAM1"      
## [16] "SAMD3"       "PRSS23"      "GAS7"        "PARP8"       "CBLB"       
## [21] "MYBL1"       "NCALD"       "ARHGAP26"    "JAZF1"       "ABCB1"      
## [26] "SYTL2"       "PPP2R2B"     "PLCB1"       "MIR4435-2HG" "TPRG1"      
## [31] "DOCK5"       "EFNA5"       "ARHGEF28"    "DGKK"       
## 
## $brown
##  [1] "INPP4B"     "PAG1"       "CAMK4"      "ANK3"       "CDC14A"    
##  [6] "ARHGAP15"   "PRKCA"      "LEF1"       "ADAM19"     "BCL2"      
## [11] "TTC39C"     "MGAT5"      "MAP3K1"     "MDFIC"      "HIVEP2"    
## [16] "GNAQ"       "NR3C2"      "DOCK10"     "AC139720.1" "MAML2"     
## [21] "DPP4"       "CMTM8"      "TAB2"       "KANK1"      "TXK"       
## [26] "PDE4B"      "DISC1"      "THEMIS"    
## 
## $turquoise
##  [1] "RPL13"      "RPLP2"      "RPL34"      "RPL28"      "RPL13A"    
##  [6] "RPS19"      "TMSB10"     "RPL41"      "RPL38"      "RPS28"     
## [11] "JUN"        "RPL3"       "RPLP1"      "RPS18"      "FOS"       
## [16] "RPS8"       "RPS2"       "RPS12"      "RPL18A"     "FOSB"      
## [21] "RPS23"      "JUNB"       "AC022217.3" "TUBA1A"     "IER2"      
## [26] "AC079793.1" "TEX14"      "NAMPT"      "EGR1"       "IFRD1"     
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
##  [1] "ZEB2"        "AOAH"        "C1orf21"     "GNLY"        "OSBPL5"     
##  [6] "LYN"         "SGCD"        "TGFBR3"      "KLRC3"       "IKZF2"      
## [11] "SETBP1"      "TPST2"       "AGAP1"       "AC093865.1"  "NCAM1"      
## [16] "SAMD3"       "PRSS23"      "GAS7"        "PARP8"       "CBLB"       
## [21] "MYBL1"       "NCALD"       "ARHGAP26"    "JAZF1"       "ABCB1"      
## [26] "SYTL2"       "PPP2R2B"     "PLCB1"       "MIR4435-2HG" "TPRG1"      
## [31] "DOCK5"       "EFNA5"       "ARHGEF28"    "DGKK"       
## 
## $brown
##  [1] "INPP4B"     "PAG1"       "CAMK4"      "ANK3"       "CDC14A"    
##  [6] "ARHGAP15"   "PRKCA"      "LEF1"       "ADAM19"     "BCL2"      
## [11] "TTC39C"     "MGAT5"      "MAP3K1"     "MDFIC"      "HIVEP2"    
## [16] "GNAQ"       "NR3C2"      "DOCK10"     "AC139720.1" "MAML2"     
## [21] "DPP4"       "CMTM8"      "TAB2"       "KANK1"      "TXK"       
## [26] "PDE4B"      "DISC1"      "THEMIS"    
## 
## $turquoise
##  [1] "RPL13"      "RPLP2"      "RPL34"      "RPL28"      "RPL13A"    
##  [6] "RPS19"      "TMSB10"     "RPL41"      "RPL38"      "RPS28"     
## [11] "JUN"        "RPL3"       "RPLP1"      "RPS18"      "FOS"       
## [16] "RPS8"       "RPS2"       "RPS12"      "RPL18A"     "FOSB"      
## [21] "RPS23"      "JUNB"       "AC022217.3" "TUBA1A"     "IER2"      
## [26] "AC079793.1" "TEX14"      "NAMPT"      "EGR1"       "IFRD1"     
## 
## [1] "5020_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.3687
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49949
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.4344e-15
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  RPS27, RPLP1, RPLP2, RPL41, TTN, ASTN2, XIST, TSHR, KRT72, FHIT 
##     LINC01259, GOLGA6L4, AL162493.1, LARGE1, AL049828.1, LMTK3, AC130324.2, PLGRKT, TNNC2, ALDH7A1 
## Negative:  SLC38A1, EML4, MLLT10, ATF2, ARHGAP15, KLF12, NFKB1, YPEL1, DENND1B, BABAM2 
##     FOXO1, STK39, MBNL1, C5orf56, BCKDHB, ATP8A1, FNDC3B, DYM, AUH, FYN 
## PC_ 2 
## Positive:  ZEB2, KLRC3, KLRF1, SGCD, IRF8, KLRD1, AOAH, AL392086.3, OSBPL5, CTBP2 
##     PDGFD, C1orf21, NCALD, SETBP1, AC024028.1, IKZF2, ABI3, LYN, MTSS1, GNLY 
## Negative:  INPP4B, PRKCA, ANK3, CDC14A, CAMK4, TSHZ2, BCL2, LEF1, PLCL1, ARHGAP15 
##     PAG1, FAAH2, MAP3K1, GNAQ, IGF1R, BACH2, NELL2, FMN1, MGAT5, SNX9 
## PC_ 3 
## Positive:  LINC02694, TOX, IL34, ST8SIA6, AC105429.1, CCDC141, SEMA3G, TTN, AC093865.1, LINC02062 
##     AL135978.2, ATG4C, PIGM, MCF2L2, MIR4435-2HG, CDHR3, SMC4, LINC01727, MIR181A1HG, KIF20B 
## Negative:  RBMS1, PDE4D, PLCB1, NFKB1, TNFAIP3, A2M, ANK3, BACH2, RPL41, RPLP1 
##     IGF1R, PELI2, TAFA1, RPLP2, MAP3K4, EDA, ADGRE5, LINC00612, PCSK5, NR3C2 
## PC_ 4 
## Positive:  PLCB1, PDE4D, MYBL1, PTPN13, ADAM12, SLC4A10, LINC00299, AC104211.1, HMGCS1, CMIP 
##     GNG2, NTN4, MSC-AS1, NIBAN1, IL18RAP, TNFAIP3, TGFBR3, CATSPERG, MB21D2, NECTIN2 
## Negative:  CERS6, APBA2, LEF1, CDC7, AL392086.3, EPHX4, BHLHE40-AS1, C4orf50, SKIL, TSHZ2 
##     FHIT, B3GAT1, RNF43, KLRC3, ALG10, PTGDR, TXK, WDR63, KLRF1, IRF8 
## PC_ 5 
## Positive:  AC025188.1, FOS, RPL41, JUN, LINC00513, FOSB, RORA-AS1, TRIM69, TOX, PLCG2 
##     RGCC, AC093583.1, RPLP1, AC013652.1, TNFRSF9, LMNA, LOXL1, RAB11A, AL691403.1, AC092640.1 
## Negative:  ETV6, HK1, ADAMTS17, FLACC1, PHLDB2, PNPLA1, SFMBT2, WDR64, TTLL1, FAM174B 
##     CELF2, MTAP, TSHZ2, PARL, ABCA10, PRR5, STX18-AS1, USP13, WWTR1, LYN 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1  0.22400 11.500         0.5160 110.0000  1.10e+02 115.000
## 2      2  0.00131  0.338         0.5370  57.1000  5.71e+01  63.700
## 3      3  0.17200 -2.880         0.7270  30.1000  3.00e+01  36.300
## 4      4  0.34700 -3.250         0.7300  16.0000  1.59e+01  21.400
## 5      5  0.51200 -3.240         0.7090   8.6800  8.52e+00  13.100
## 6      6  0.56900 -3.200         0.6870   4.7700  4.60e+00   8.240
## 7      7  0.61800 -2.810         0.6320   2.6700  2.53e+00   5.400
## 8      8  0.70500 -2.520         0.7180   1.5200  1.40e+00   3.700
## 9      9  0.77300 -2.460         0.7210   0.8880  7.82e-01   2.620
## 10    10  0.84700 -2.350         0.8040   0.5300  4.45e-01   1.900
## 11    12  0.94200 -2.070         0.9370   0.2030  1.49e-01   1.070
## 12    14  0.85700 -1.800         0.8620   0.0868  4.98e-02   0.647
## 13    16  0.27500 -3.030         0.1370   0.0411  1.78e-02   0.409
## 14    18  0.19800 -2.310        -0.0301   0.0212  6.38e-03   0.267
## 15    20  0.23500 -2.280         0.0343   0.0118  2.48e-03   0.180

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5 
## 143  19  16  13  12  11

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 6 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.

## $yellow
##  [1] "EML4"   "FOXO1"  "DPYD"   "INPP4B" "PRKCA"  "ANK3"   "CDC14A" "PAG1"  
##  [9] "FAAH2"  "GNAQ"   "FMN1"   "MGAT5" 
## 
## $brown
##  [1] "ARHGAP15" "NFKB1"    "BCL2"     "BACH2"    "SNX9"     "RBMS1"   
##  [7] "PCSK5"    "PDE4D"    "PLCB1"    "TNFAIP3"  "PELI2"    "GREM2"   
## [13] "RORA"    
## 
## $blue
##  [1] "YPEL1"       "ZEB2"        "KLRC3"       "KLRF1"       "SGCD"       
##  [6] "IRF8"        "KLRD1"       "AOAH"        "AL392086.3"  "OSBPL5"     
## [11] "CTBP2"       "PDGFD"       "C1orf21"     "NCALD"       "SETBP1"     
## [16] "AC024028.1"  "ABI3"        "LYN"         "MTSS1"       "GNLY"       
## [21] "B3GAT1"      "SLC4A4"      "PTGDR"       "BHLHE40-AS1" "AC018816.1" 
## [26] "AC068631.1"  "CDC7"        "EPHX4"       "SKIL"        "RNF43"      
## [31] "ALG10"       "WDR63"       "LINC00469"   "TSHZ3"       "STX18-AS1"  
## 
## $green
##  [1] "BCKDHB"     "IL34"       "ST8SIA6"    "PIGM"       "PDE1B"     
##  [6] "AC093583.1" "TNFRSF9"    "AC092640.1" "HEATR6"     "LINC02803" 
## [11] "RHBDD3"    
## 
## [1] "275/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "63/10000 permutations failed the Mann-Whitney test."
## $yellow
##  [1] "EML4"   "FOXO1"  "DPYD"   "INPP4B" "PRKCA"  "ANK3"   "CDC14A" "PAG1"  
##  [9] "FAAH2"  "GNAQ"   "FMN1"   "MGAT5" 
## 
## $brown
##  [1] "ARHGAP15" "NFKB1"    "BCL2"     "BACH2"    "SNX9"     "RBMS1"   
##  [7] "PCSK5"    "PDE4D"    "PLCB1"    "TNFAIP3"  "PELI2"    "GREM2"   
## [13] "RORA"    
## 
## $blue
##  [1] "YPEL1"       "ZEB2"        "KLRC3"       "KLRF1"       "SGCD"       
##  [6] "IRF8"        "KLRD1"       "AOAH"        "AL392086.3"  "OSBPL5"     
## [11] "CTBP2"       "PDGFD"       "C1orf21"     "NCALD"       "SETBP1"     
## [16] "AC024028.1"  "ABI3"        "LYN"         "MTSS1"       "GNLY"       
## [21] "B3GAT1"      "SLC4A4"      "PTGDR"       "BHLHE40-AS1" "AC018816.1" 
## [26] "AC068631.1"  "CDC7"        "EPHX4"       "SKIL"        "RNF43"      
## [31] "ALG10"       "WDR63"       "LINC00469"   "TSHZ3"       "STX18-AS1"  
## 
## $green
##  [1] "BCKDHB"     "IL34"       "ST8SIA6"    "PIGM"       "PDE1B"     
##  [6] "AC093583.1" "TNFRSF9"    "AC092640.1" "HEATR6"     "LINC02803" 
## [11] "RHBDD3"
saveRDS(mods1, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230601CD4Modules_Participant_Timepoint.rds")

results$T_TP<-paste(results$Treatment, results$Timepoint, sep="_")
results.split<-SplitObject(results, "T_TP")
#in this case just doing one documented iteration as long as the softpower is <9, otherwise setting to 8 
#module set here is pretty unspectatular relative to the individual defined ones. Likely not worth analyzing further 
conds<-cbind(c(5,5,4,5,5,7),c(7,8,8,8,8,8))
mods1.5<-WrapGroupModID(results.split, "NA",conds)
## [1] "Bup.Nalo_0"
## PC_ 1 
## Positive:  ZEB2, AFF3, AC105402.3, AOAH, VCAN, IGKC, RPL41, PLXDC2, HDAC9, CDK14 
##     IGHM, SETBP1, RPL13, UBE2E2, MTRNR2L8, RPLP2, GNLY, NKG7, CCL5, ACTB 
## Negative:  INPP4B, CAMK4, PAG1, SERINC5, CDC14A, CASK, ARHGAP15, ANK3, RORA, HIVEP2 
##     MDFIC, DOCK10, LEF1, KLF12, PRKCA, SKAP1, AKT3, GPRIN3, RASGRF2, MAML2 
## PC_ 2 
## Positive:  TSHZ2, LEF1, FHIT, PLCL1, LTB, TTN, RPL13, SESN3, RPLP2, F5 
##     PRKCA, EEF1A1, RTKN2, MAP3K1, TXK, GCNT4, FAM13A, RPL41, TMSB10, LDLRAD4 
## Negative:  TGFBR3, C1orf21, AOAH, ZEB2, PPP2R2B, PLCB1, PDGFD, MYBL1, SYTL2, STAT4 
##     AGAP1, PARP8, NCALD, AC243829.2, THEMIS, DTHD1, GTDC1, A2M, PZP, LINC00299 
## PC_ 3 
## Positive:  NELL2, ANK3, NR3C2, AC105402.3, RASGRF2, PRKCA, AC139720.1, PCSK5, BCL2, MTRNR2L8 
##     PRKN, SBF2, EDA, MAN1C1, IGF1R, SATB1-AS1, ADAM23, TXK, TAFA1, RNF157 
## Negative:  LINC02694, IKZF2, AC013652.1, TOX, AC093865.1, TTN, CDHR3, STAM, CCDC141, ST8SIA6 
##     RTKN2, DUSP4, MIR4435-2HG, TSHR, NIBAN1, HPGD, ATXN7L1, F5, MIR181A1HG, IL2RA 
## PC_ 4 
## Positive:  PLXDC2, AFF3, VCAN, UBE2E2, HDAC9, CDK14, MTSS1, ZEB2, TCF7L2, AC105402.3 
##     CCSER1, MAML3, PDE4D, ALOX5, GAB2, CTBP2, FRY, VAV3, ZSWIM6, MAP3K1 
## Negative:  LINC01934, IFNG-AS1, ST8SIA1, ANK3, ITGA4, LRIG1, BICDL1, INPP4B, IL18RAP, THEMIS 
##     TPRG1, PCAT1, RASGRF2, GNAO1, SGPP2, RORA, FMN1, IL12RB2, SKAP1, MYBL1 
## PC_ 5 
## Positive:  AL353660.1, GCNT4, ST8SIA1, TOX, AOAH, SESN3, RBMS3, TXK, LINC01934, C12orf42 
##     VAV3, SGPP2, TAFA2, KCNQ5, LEF1, MAML2, UBASH3B, IKZF2, SH3RF3, TRPS1 
## Negative:  FRY, ADAM12, LINC00299, RUNX2, PTPN13, ADAM19, CCR6, IL32, EEF1A1, PLD1 
##     LTB, B4GALT5, RPS19, LINC02694, AC013652.1, RPL13, PLCB1, MCF2L2, RBMS1, IL18R1 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1   0.3100 13.400         0.8680 88.70000  8.89e+01 93.0000
## 2      2   0.1290  3.850         0.7940 45.60000  4.56e+01 50.4000
## 3      3   0.0042 -0.428         0.7500 23.60000  2.34e+01 27.9000
## 4      4   0.1370 -2.000         0.6030 12.30000  1.21e+01 15.7000
## 5      5   0.3850 -2.840         0.7550  6.47000  6.27e+00  9.0400
## 6      6   0.6200 -3.200         0.7870  3.43000  3.26e+00  5.2700
## 7      7   0.8230 -3.510         0.8670  1.83000  1.71e+00  3.1200
## 8      8   0.8930 -3.640         0.9090  0.99000  9.13e-01  1.8700
## 9      9   0.8730 -3.510         0.8660  0.53900  4.91e-01  1.1300
## 10    10   0.8820 -3.230         0.8670  0.29700  2.62e-01  0.6930
## 11    12   0.8900 -2.870         0.8760  0.09260  7.93e-02  0.2670
## 12    14   0.9610 -2.350         0.9660  0.03020  2.37e-02  0.1060
## 13    16   0.9010 -2.070         0.8870  0.01030  7.27e-03  0.0430
## 14    18   0.2370 -3.530         0.0311  0.00373  2.33e-03  0.0208
## 15    20   0.3470 -5.610         0.1820  0.00142  7.79e-04  0.0120

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4 
## 121  21  13  10  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 3 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 3 module eigengenes in given set.

## $yellow
##  [1] "INPP4B"     "CAMK4"      "PAG1"       "SERINC5"    "CDC14A"    
##  [6] "CASK"       "ARHGAP15"   "ANK3"       "RORA"       "HIVEP2"    
## [11] "MDFIC"      "DOCK10"     "LEF1"       "KLF12"      "PRKCA"     
## [16] "AKT3"       "RASGRF2"    "MAML2"      "FAAH2"      "PDE3B"     
## [21] "SOS1"       "SESN3"      "TXK"        "CMTM8"      "NELL2"     
## [26] "NR3C2"      "AC139720.1" "BCL2"       "MAN1C1"     "TAFA1"     
## [31] "RNF157"     "DPP4"       "GREM2"      "ST8SIA1"    "LRIG1"     
## [36] "PCAT1"      "AL353660.1" "AC233976.1" "ADAM19"     "RBMS1"     
## [41] "MB21D2"    
## 
## $blue
##  [1] "TTN"        "RTKN2"      "STAM"       "CCDC141"    "LINC02694" 
##  [6] "IKZF2"      "AC013652.1" "AC093865.1" "CDHR3"      "ST8SIA6"   
## [11] "DUSP4"      "TSHR"       "IL2RA"     
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $yellow
##  [1] "INPP4B"     "CAMK4"      "PAG1"       "SERINC5"    "CDC14A"    
##  [6] "CASK"       "ARHGAP15"   "ANK3"       "RORA"       "HIVEP2"    
## [11] "MDFIC"      "DOCK10"     "LEF1"       "KLF12"      "PRKCA"     
## [16] "AKT3"       "RASGRF2"    "MAML2"      "FAAH2"      "PDE3B"     
## [21] "SOS1"       "SESN3"      "TXK"        "CMTM8"      "NELL2"     
## [26] "NR3C2"      "AC139720.1" "BCL2"       "MAN1C1"     "TAFA1"     
## [31] "RNF157"     "DPP4"       "GREM2"      "ST8SIA1"    "LRIG1"     
## [36] "PCAT1"      "AL353660.1" "AC233976.1" "ADAM19"     "RBMS1"     
## [41] "MB21D2"    
## 
## $blue
##  [1] "TTN"        "RTKN2"      "STAM"       "CCDC141"    "LINC02694" 
##  [6] "IKZF2"      "AC013652.1" "AC093865.1" "CDHR3"      "ST8SIA6"   
## [11] "DUSP4"      "TSHR"       "IL2RA"     
## 
## [1] "Bup.Nalo_3"
## PC_ 1 
## Positive:  RPL13, RPL41, RPS18, RPLP2, TMSB10, RPS19, LTB, TTN, AC093865.1, IKZF2 
##     CCDC141, XIST, RTKN2, TRBC1, MTRNR2L8, JUN, ENTPD1, F5, TSHZ2, CDHR3 
## Negative:  PARP8, THEMIS, ANK3, ARHGAP15, RBMS1, RORA, PLCB1, NR3C2, CDC14A, LINC01619 
##     MBNL1, PPP3CA, INPP4B, CBLB, ZBTB20, RASGRF2, MYBL1, MCTP2, ANTXR2, FKBP5 
## PC_ 2 
## Positive:  STAM, IKZF2, PLCL1, CCDC141, AC093865.1, TTN, CDHR3, LDLRAD4, LINC02694, TSHZ2 
##     IL2RA, GNAQ, TOX, ZC2HC1A, MCF2L2, PKIA, RTKN2, SNED1, ATXN7L1, F5 
## Negative:  PLCB1, ZEB2, AOAH, ARHGAP26, AC105402.3, IFNG-AS1, C1orf21, CCL5, MVB12B, IL18RAP 
##     A2M, AGAP1, MCTP2, GNLY, MYBL1, PZP, THEMIS, YES1, PPP2R2B, DTHD1 
## PC_ 3 
## Positive:  ZEB2, LINC02694, ARHGAP26, NIBAN1, IKZF2, C1orf21, AC093865.1, MIR4435-2HG, SAMD3, TOX 
##     GNLY, PPP2R2B, TGFBR3, ST8SIA6, AOAH, NCALD, CCDC141, AC013652.1, PDGFD, DTHD1 
## Negative:  PRKCA, ANK3, INPP4B, TXK, AC139720.1, CMTM8, NELL2, LEF1, AC233976.1, SESN3 
##     PCSK5, AL353660.1, BCL2, RPL13, BACH2, FAAH2, LTB, RPLP2, ADAMTS17, TSHZ2 
## PC_ 4 
## Positive:  XIST, ITGA4, CNOT6L, MCOLN2, STAT1, ST8SIA1, FMN1, SESN3, AP000787.1, ANK3 
##     PDE4B, ARHGAP15, LTB, HIVEP3, ESR1, IL12RB2, LINC01934, PHACTR2, SLC9A9, ASAP1 
## Negative:  AC105402.3, MTRNR2L8, SAMD12, AL589693.1, NR3C2, RUNX2, IL2RA, KANK1, AL136456.1, ADAM23 
##     LINC00278, PRKN, GREM2, SETD7, ZNF516, ADAM12, RNF157, SLC16A10, BANK1, IKZF2 
## PC_ 5 
## Positive:  ADAM19, PAG1, LINC02694, KAT2B, ADAM12, NIBAN1, RORA, AC013652.1, FRY, LRIG1 
##     RUNX2, LINC00299, B4GALT5, MB21D2, CCR6, KIAA0825, CDC14A, SNED1, DPP4, PLD1 
## Negative:  LYN, BANK1, RALGPS2, CDK14, FCRL1, EBF1, HDAC9, OSBPL10, WDFY4, AFF3 
##     TRIO, PIK3AP1, RRM2, ARHGAP24, ZEB2, TCF4, USP6NL, PLXDC2, MEF2C, COBLL1 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1 0.044900  9.580        0.89100 90.50000  9.04e+01 94.6000
## 2      2 0.093900  7.590        0.71500 46.40000  4.63e+01 50.8000
## 3      3 0.171000 26.700        0.02710 24.00000  2.38e+01 27.5000
## 4      4 0.020000  1.570        0.77000 12.50000  1.23e+01 15.2000
## 5      5 0.000153  0.102        0.84600  6.60000  6.50e+00  8.5900
## 6      6 0.018500 -0.919        0.92900  3.51000  3.44e+00  4.9200
## 7      7 0.155000 -2.020        0.88900  1.89000  1.83e+00  2.8600
## 8      8 0.200000 -1.640        0.79400  1.03000  9.84e-01  1.6800
## 9      9 0.505000 -2.110        0.70300  0.57100  5.34e-01  1.0900
## 10    10 0.811000 -2.710        0.77500  0.32100  2.92e-01  0.7850
## 11    12 0.262000 -6.450        0.06270  0.10700  8.95e-02  0.4460
## 12    14 0.202000 -3.310        0.01270  0.03940  2.84e-02  0.2720
## 13    16 0.178000 -3.380        0.01330  0.01610  8.94e-03  0.1710
## 14    18 0.187000 -2.920       -0.00558  0.00730  2.90e-03  0.1100
## 15    20 0.021800 -1.040        0.07970  0.00366  9.74e-04  0.0708

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## [1] "No module detected"
## dynamicMods
##   0 
## 179

## Error in hclust(as.dist(MEDiss), method = "average") : 
##   The distance structure is empty.
## [1] "Naltrexone_3"
## PC_ 1 
## Positive:  INPP4B, PAG1, PRKCA, ANK3, ARHGAP15, LEF1, CDC14A, MAP3K1, ADAM19, MGAT5 
##     BCL2, HIVEP2, TSHZ2, FAAH2, CASK, PLCL1, CMTM8, AC139720.1, SAMD12, BACH2 
## Negative:  ZEB2, C1orf21, AOAH, GNLY, SETBP1, OSBPL5, TGFBR3, ARHGAP26, LINC02384, AGAP1 
##     AC105402.3, PDGFD, MTRNR2L8, SYTL3, KLRD1, PPP2R2B, LYN, KLRK1, AC243829.2, MYO3B 
## PC_ 2 
## Positive:  RPL13, RPLP2, RPS18, RPL13A, RPS28, RPLP1, RPL41, RPL28, RPS23, MTRNR2L8 
##     RPS19, RPS12, JUN, RPS2, FOS, LTB, FOSB, TSHZ2, JUNB, IER2 
## Negative:  PARP8, CBLB, ZEB2, MCTP2, C1orf21, MBNL1, TGFBR3, RORA, JAZF1, NCALD 
##     ARHGAP26, PPP3CA, MYBL1, CEMIP2, PPP2R2B, NIBAN1, LINC00278, PAM, PDGFD, LINC02384 
## PC_ 3 
## Positive:  LINC02694, TTN, CCDC141, ENTPD1, IKZF2, RTKN2, STAM, AC093865.1, AC013652.1, TOX 
##     CDHR3, MIR181A1HG, IL2RA, HPGD, ZC2HC1A, F5, HACD1, BARD1, EZH2, DLEU2 
## Negative:  PLCB1, ANK3, NR3C2, RASGRF2, MYBL1, BACH2, THEMIS, PCSK5, BTBD11, NELL2 
##     ATP10A, TAFA1, RBMS1, SBF2, PELI2, IGF1R, EDA, PDE4D, DPP4, APBA2 
## PC_ 4 
## Positive:  FOSB, FOS, JUN, RPS2, RPL13, RPLP2, RPS28, RPS12, RPLP1, RPL41 
##     RPL28, JUNB, RPS23, RPS19, RPS18, AC022217.3, LTB, RPL13A, IER2, EGR1 
## Negative:  FRY, PTPN13, AC105402.3, ADAM19, LINC00299, ADAM12, TANC1, MCF2L2, CCR6, LINC02649 
##     B4GALT5, AL589693.1, COL5A3, KIF5C, AFDN, FKBP5, AL136456.1, RORA, MYBL1, MTRNR2L8 
## PC_ 5 
## Positive:  IKZF2, AC093865.1, TTN, ATXN7L1, CDHR3, ARID5B, LEF1, ST8SIA1, UBASH3B, RTKN2 
##     CCDC141, FCRL3, KLRC3, TOX, SESN3, AOAH, GCNT4, AL353660.1, LINC01727, APBA2 
## Negative:  RRM2, POLQ, NUSAP1, DIAPH3, MKI67, FAM111B, DTL, KIF18B, CENPU, SHCBP1 
##     TTK, CDC45, NCAPG, CLSPN, ANLN, SPC25, NCAPG2, E2F7, ASPM, ECT2 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k. max.k.
## 1      1   0.1490 13.900        0.56900 80.60000  80.50000 85.400
## 2      2   0.1770  7.670        0.58100 41.90000  42.00000 46.900
## 3      3   0.1250  4.130        0.67500 22.20000  22.10000 26.300
## 4      4   0.0133  0.879        0.83500 11.90000  11.80000 15.100
## 5      5   0.0130 -0.546        0.75800  6.49000   6.44000  8.760
## 6      6   0.3070 -2.450        0.94600  3.61000   3.55000  5.690
## 7      7   0.4430 -2.750        0.73600  2.04000   1.98000  3.830
## 8      8   0.6190 -2.690        0.76300  1.18000   1.12000  2.640
## 9      9   0.7300 -2.620        0.79700  0.69600   0.63700  1.860
## 10    10   0.7800 -2.430        0.74800  0.41900   0.36900  1.330
## 11    12   0.2950 -5.860        0.11500  0.16300   0.12800  0.708
## 12    14   0.2290 -4.320        0.01960  0.06920   0.04600  0.454
## 13    16   0.2200 -3.710       -0.00229  0.03230   0.01670  0.309
## 14    18   0.3250 -4.000        0.23400  0.01640   0.00626  0.218
## 15    20   0.3440 -4.700        0.16900  0.00908   0.00239  0.158

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  0  1  2  3  4  5  6  7 
## 70 15 14 13 13 12 11 10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.

## $black
##  [1] "INPP4B"     "PAG1"       "PRKCA"      "ANK3"       "ARHGAP15"  
##  [6] "LEF1"       "CDC14A"     "MAP3K1"     "ADAM19"     "MGAT5"     
## [11] "BCL2"       "HIVEP2"     "TSHZ2"      "FAAH2"      "CASK"      
## [16] "PLCL1"      "CMTM8"      "AC139720.1" "SAMD12"     "ACVR1"     
## [21] "TXK"        "NR3C2"      "MDFIC"      "RASGRF2"    "DPP4"      
## 
## $brown
##  [1] "ZEB2"       "C1orf21"    "AOAH"       "GNLY"       "SETBP1"    
##  [6] "OSBPL5"     "TGFBR3"     "ARHGAP26"   "LINC02384"  "AGAP1"     
## [11] "PDGFD"      "SYTL3"      "KLRD1"      "PPP2R2B"    "LYN"       
## [16] "KLRK1"      "AC243829.2" "PRSS23"     "TMCC3"      "MCTP2"     
## [21] "SGCD"       "NCALD"      "MYBL1"      "DNAJC1"     "PLCB1"     
## 
## $blue
##  [1] "RPL13"      "RPLP2"      "RPS18"      "RPL13A"     "RPS28"     
##  [6] "RPLP1"      "RPL41"      "RPL28"      "RPS23"      "RPS19"     
## [11] "RPS12"      "JUN"        "RPS2"       "FOS"        "LTB"       
## [16] "FOSB"       "JUNB"       "IER2"       "AC022217.3" "EGR1"      
## [21] "TEX14"      "DNAJA1"     "AC253572.2" "IFRD1"      "EIF4A3"    
## 
## $yellow
##  [1] "LINC02694"  "TTN"        "CCDC141"    "ENTPD1"     "IKZF2"     
##  [6] "RTKN2"      "STAM"       "AC093865.1" "AC013652.1" "IL2RA"     
## [11] "HPGD"       "ZC2HC1A"    "HACD1"     
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $black
##  [1] "INPP4B"     "PAG1"       "PRKCA"      "ANK3"       "ARHGAP15"  
##  [6] "LEF1"       "CDC14A"     "MAP3K1"     "ADAM19"     "MGAT5"     
## [11] "BCL2"       "HIVEP2"     "TSHZ2"      "FAAH2"      "CASK"      
## [16] "PLCL1"      "CMTM8"      "AC139720.1" "SAMD12"     "ACVR1"     
## [21] "TXK"        "NR3C2"      "MDFIC"      "RASGRF2"    "DPP4"      
## 
## $brown
##  [1] "ZEB2"       "C1orf21"    "AOAH"       "GNLY"       "SETBP1"    
##  [6] "OSBPL5"     "TGFBR3"     "ARHGAP26"   "LINC02384"  "AGAP1"     
## [11] "PDGFD"      "SYTL3"      "KLRD1"      "PPP2R2B"    "LYN"       
## [16] "KLRK1"      "AC243829.2" "PRSS23"     "TMCC3"      "MCTP2"     
## [21] "SGCD"       "NCALD"      "MYBL1"      "DNAJC1"     "PLCB1"     
## 
## $blue
##  [1] "RPL13"      "RPLP2"      "RPS18"      "RPL13A"     "RPS28"     
##  [6] "RPLP1"      "RPL41"      "RPL28"      "RPS23"      "RPS19"     
## [11] "RPS12"      "JUN"        "RPS2"       "FOS"        "LTB"       
## [16] "FOSB"       "JUNB"       "IER2"       "AC022217.3" "EGR1"      
## [21] "TEX14"      "DNAJA1"     "AC253572.2" "IFRD1"      "EIF4A3"    
## 
## $yellow
##  [1] "LINC02694"  "TTN"        "CCDC141"    "ENTPD1"     "IKZF2"     
##  [6] "RTKN2"      "STAM"       "AC093865.1" "AC013652.1" "IL2RA"     
## [11] "HPGD"       "ZC2HC1A"    "HACD1"     
## 
## [1] "Naltrexone_0"
## PC_ 1 
## Positive:  RPLP2, RPL13, MTRNR2L8, RPS23, RPL41, RPS18, RPS12, FOS, JUN, FOSB 
##     IER2, JUNB, AC022217.3, AL691403.1, EGR1, AC103591.3, CSKMT, SH3RF3, TTN, AFF3 
## Negative:  ARHGAP15, RORA, LINC01619, MBNL1, GPRIN3, SOS1, PAG1, PARP8, RABGAP1L, CDC14A 
##     FRY, RBMS1, INPP4B, RUNX2, MGAT5, PPP3CA, CBLB, ADAM19, THEMIS, ARL15 
## PC_ 2 
## Positive:  INPP4B, PRKCA, ANK3, LEF1, PAG1, BCL2, TSHZ2, BACH2, MAML2, PLCL1 
##     CDC14A, XIST, CMTM8, NELL2, ARHGAP15, RPL13, MGAT5, FAAH2, FMN1, RPLP2 
## Negative:  ZEB2, C1orf21, AOAH, GNLY, SYNE1, SETBP1, LINC02384, AC243829.2, PDGFD, OSBPL5 
##     KLRD1, PRSS23, TGFBR3, SAMD3, KLRK1, LYN, ADGRG5, ARHGAP26, PPP2R2B, KLRC3 
## PC_ 3 
## Positive:  LINC02694, STAM, ENTPD1, AC013652.1, TTN, MCF2L2, RTKN2, DUSP4, CCDC141, IL2RA 
##     NIBAN1, HPGD, ZC2HC1A, AC093865.1, PALM2-AKAP2, IKZF2, EZH2, MIR181A1HG, BARD1, KIF20B 
## Negative:  NELL2, IGF1R, RASGRF2, BACH2, NR3C2, PCSK5, PLCB1, AOAH, MCTP2, TAFA1 
##     C1orf21, RPL41, RPS23, PRKN, RPS12, SBF2, ANK3, RPL13, RPLP2, RPS18 
## PC_ 4 
## Positive:  FRY, PDE4D, PTPN13, ADAM12, PLCB1, ADAM19, LINC00299, MYBL1, BTBD11, LATS2 
##     AL136456.1, RORA, CR1, MB21D2, ELOVL4, SOS1, AUTS2, CCR6, ALOX5, AL589693.1 
## Negative:  IKZF2, FOSB, LEF1, JUN, FOS, TOX, RPL41, AC093865.1, RPS23, AC022217.3 
##     TTN, MBNL1, CCDC141, RPS12, RPL13, RPLP2, RPS18, SESN3, PLCG2, JUNB 
## PC_ 5 
## Positive:  UBASH3B, FAAH2, CMTM8, AL353660.1, TSHZ2, GRK5, AC139720.1, ST8SIA1, LEF1, FKBP5 
##     AK5, AC233976.1, IFNG-AS1, TMEM45B, DISC1, ATXN7L1, MAML2, SLC22A23, ADAMTS17, SORCS3 
## Negative:  JUN, FOSB, FOS, AC022217.3, DNAJA1, JUNB, IER2, RPL41, RPS12, RPS23 
##     ANXA1, AL691403.1, RPS18, RPLP2, RPL13, EGR1, AL606489.1, TEX14, NAMPT, PDE4D 
##    Power SFT.R.sq   slope truncated.R.sq  mean.k. median.k. max.k.
## 1      1 2.02e-01 62.6000        0.07410 84.90000  84.60000 90.100
## 2      2 1.80e-01 28.8000        0.04210 43.80000  43.50000 49.600
## 3      3 1.65e-01 17.9000        0.01190 22.90000  22.60000 27.700
## 4      4 4.26e-03  0.5410        0.78400 12.00000  11.90000 15.700
## 5      5 7.62e-05 -0.0555        0.87800  6.43000   6.37000  8.980
## 6      6 6.37e-04 -0.1230        0.95300  3.47000   3.42000  5.230
## 7      7 6.17e-03 -0.2620        0.81900  1.90000   1.86000  3.080
## 8      8 1.26e-01 -1.0700        0.58700  1.06000   1.02000  1.970
## 9      9 2.69e-01 -1.4700        0.20000  0.60200   0.55700  1.300
## 10    10 5.48e-01 -1.8200        0.42700  0.34900   0.31100  0.939
## 11    12 7.71e-01 -1.9200        0.76200  0.12500   0.09770  0.558
## 12    14 4.35e-02 -1.4100        0.01180  0.05020   0.03200  0.356
## 13    16 6.83e-01 -1.3800        0.82100  0.02250   0.01120  0.235
## 14    18 1.00e-01 -1.6000       -0.00218  0.01120   0.00373  0.158
## 15    20 2.05e-01 -2.0100       -0.01970  0.00612   0.00129  0.107

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1 
## 149  18

## Error in graphics:::plotHclust(n1, merge, height, order(x$order), hang,  : 
##   invalid dendrogram input
## [1] "Methadone_3"
## PC_ 1 
## Positive:  RPL13, RPLP2, RPLP1, RPS18, RPS27, RPL41, RPS2, JUN, FOS, FOSB 
##     AC243829.2, C1orf21, NKG7, AC022217.3, GNLY, FMN1, CLNK, RBFOX3, LYN, EPDR1 
## Negative:  ARHGAP15, MBNL1, RORA, INPP4B, DPYD, ZBTB20, THEMIS, CDC14A, MDFIC, GPRIN3 
##     TNFAIP8, ANTXR2, HIVEP2, PLCG2, DOCK10, RABGAP1L, RBMS1, MGAT5, MAML2, PHACTR2 
## PC_ 2 
## Positive:  ZEB2, GNLY, AOAH, SETBP1, KLRD1, AC243829.2, SAMD3, SYNE1, PDGFD, C1orf21 
##     KLRK1, TGFBR3, OSBPL5, ARHGAP26, LINC02384, PLEK, PPP2R2B, ADGRG5, VAV3, ATP8B4 
## Negative:  PRKCA, ANK3, LEF1, INPP4B, TSHZ2, BCL2, MGAT5, BACH2, NR3C2, NELL2 
##     FAAH2, CDC14A, CMTM8, RPL13, AC139720.1, GNAQ, RASGRF2, PCSK5, RPS18, HIVEP2 
## PC_ 3 
## Positive:  LINC02694, ASPM, DIAPH3, NCAPG, MIR181A1HG, RRM2, AC013652.1, KNL1, KIF18B, MKI67 
##     BUB1B, TOP2A, TTN, KIF15, E2F7, CCDC141, CDCA2, STAM, BARD1, DEPDC1B 
## Negative:  ANK3, MCTP2, TAFA1, NR3C2, PLCB1, MYBL1, NELL2, KLRD1, AOAH, RASGRF2 
##     GNLY, ZEB2, ITGA4, SBF2, ATP10A, UST, SNTB1, OSBPL5, AC243829.2, RNF144A 
## PC_ 4 
## Positive:  LINC02694, STAM, TTN, FANK1, AC013652.1, CCDC141, IKZF2, IL2RA, AC093865.1, CYTOR 
##     ATXN7L1, AL136456.1, CDHR3, MCF2L2, RTKN2, TOX, SNED1, HACD1, IL7, CTLA4 
## Negative:  DIAPH3, KIF18B, E2F7, CDCA2, KIF15, BUB1B, RRM2, KIFC1, ASPM, GTSE1 
##     DEPDC1B, MKI67, TOP2A, CDCA8, POLQ, CDC25C, CDK1, CENPI, ESPL1, ANLN 
## PC_ 5 
## Positive:  FRY, LINC00299, PTPN13, MB21D2, LINC00511, RUNX2, THEMIS, AUTS2, TSPAN18, RORA 
##     MSC-AS1, AFDN, RBMS1, B4GALT5, MCF2L2, KIAA0825, ZNF462, PLCB1, HLF, TBXAS1 
## Negative:  IKZF2, VAV3, AC093865.1, RPLP2, RPL41, RPS2, RPLP1, TOX, SESN3, RPS18 
##     RPL13, RPS27, CCDC141, AL353660.1, SLC16A10, JUN, KCNQ5, PLCL1, TENM1, FOSB 
##    Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1      1    0.015 -2.96         0.8800 93.2000  93.00000 98.200
## 2      2    0.214 -5.52         0.8410 48.5000  48.40000 54.500
## 3      3    0.418 -6.05         0.9450 25.6000  25.50000 31.400
## 4      4    0.390 -4.58         0.8750 13.7000  13.50000 18.800
## 5      5    0.552 -4.21         0.8500  7.4200   7.21000 11.800
## 6      6    0.685 -3.67         0.8200  4.1000   3.93000  7.730
## 7      7    0.758 -3.30         0.8330  2.3100   2.18000  5.270
## 8      8    0.877 -3.06         0.8890  1.3300   1.20000  3.720
## 9      9    0.916 -2.76         0.9030  0.7870   0.69100  2.700
## 10    10    0.918 -2.56         0.8960  0.4770   0.39500  2.000
## 11    12    0.921 -2.12         0.8990  0.1900   0.13400  1.160
## 12    14    0.260 -3.18         0.0646  0.0838   0.04550  0.694
## 13    16    0.253 -2.79         0.0641  0.0406   0.01630  0.426
## 14    18    0.246 -2.47         0.0574  0.0212   0.00590  0.265
## 15    20    0.240 -2.24         0.0528  0.0117   0.00216  0.167
## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
##   0   1   2   3   4 
## 123  21  14  13  11
##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $yellow
##  [1] "RPL13"      "RPLP2"      "RPLP1"      "RPS18"      "RPS27"     
##  [6] "RPL41"      "RPS2"       "JUN"        "FOS"        "FOSB"      
## [11] "AC022217.3"
## 
## $turquoise
##  [1] "AC243829.2" "C1orf21"    "GNLY"       "RBFOX3"     "SGCD"      
##  [6] "AOAH"       "ZEB2"       "SETBP1"     "KLRD1"      "SAMD3"     
## [11] "SYNE1"      "PDGFD"      "KLRK1"      "TGFBR3"     "OSBPL5"    
## [16] "ARHGAP26"   "LINC02384"  "PLEK"       "PPP2R2B"    "FAM49A"    
## [21] "DTHD1"     
## 
## $blue
##  [1] "ASPM"    "DIAPH3"  "NCAPG"   "RRM2"    "KNL1"    "KIF18B"  "MKI67"  
##  [8] "BUB1B"   "TOP2A"   "KIF15"   "E2F7"    "CDCA2"   "DEPDC1B" "MELK"   
## [15] "GTSE1"   "CENPU"   "CDK1"    "KIFC1"   "CDCA8"   "POLQ"    "CDC25C" 
## [22] "CENPI"   "ESPL1"   "ANLN"    "PCLAF"   "BRIP1"   "BRCA2"  
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $yellow
##  [1] "RPL13"      "RPLP2"      "RPLP1"      "RPS18"      "RPS27"     
##  [6] "RPL41"      "RPS2"       "JUN"        "FOS"        "FOSB"      
## [11] "AC022217.3"
## 
## $turquoise
##  [1] "AC243829.2" "C1orf21"    "GNLY"       "RBFOX3"     "SGCD"      
##  [6] "AOAH"       "ZEB2"       "SETBP1"     "KLRD1"      "SAMD3"     
## [11] "SYNE1"      "PDGFD"      "KLRK1"      "TGFBR3"     "OSBPL5"    
## [16] "ARHGAP26"   "LINC02384"  "PLEK"       "PPP2R2B"    "FAM49A"    
## [21] "DTHD1"     
## 
## $blue
##  [1] "ASPM"    "DIAPH3"  "NCAPG"   "RRM2"    "KNL1"    "KIF18B"  "MKI67"  
##  [8] "BUB1B"   "TOP2A"   "KIF15"   "E2F7"    "CDCA2"   "DEPDC1B" "MELK"   
## [15] "GTSE1"   "CENPU"   "CDK1"    "KIFC1"   "CDCA8"   "POLQ"    "CDC25C" 
## [22] "CENPI"   "ESPL1"   "ANLN"    "PCLAF"   "BRIP1"   "BRCA2"  
## 
## [1] "Methadone_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.7423
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 7.2937e-16
## PC_ 1 
## Positive:  ZEB2, AOAH, GNLY, AC243829.2, C1orf21, SETBP1, KLRD1, KLRK1, DTHD1, TGFBR3 
##     LINC02384, OSBPL5, SAMD3, TPST2, SGCD, PDGFD, SLC4A4, PPP2R2B, AL392086.3, LYN 
## Negative:  INPP4B, CAMK4, PRKCA, LEF1, ANK3, ARHGAP15, PAG1, MAP3K1, HIVEP2, MGAT5 
##     GNAQ, TSHZ2, ADAM19, FAAH2, MAML2, BCL2, CSGALNACT1, MDFIC, AC139720.1, GPRIN3 
## PC_ 2 
## Positive:  CBLB, ZEB2, RABGAP1L, ARHGAP26, TGFBR3, STAT4, SAMD3, AOAH, PARP8, C1orf21 
##     JAZF1, MCTP2, AC243829.2, NCALD, CMIP, GNLY, SYTL2, PRKCB, PPP2R2B, PAM 
## Negative:  RPLP2, RPL41, TMSB10, FOS, JUN, AC022217.3, FOSB, MTRNR2L1, PLXNA4, TSHZ2 
##     AL691403.1, PRKCA, AC103591.3, IER2, AL109930.1, FHIT, LEF1-AS1, ERCC1, TULP2, EIF4A3 
## PC_ 3 
## Positive:  LINC02694, TTN, RTKN2, CCDC141, IKZF2, AC013652.1, STAM, F5, IL2RA, CTLA4 
##     HPGD, AC093865.1, ENTPD1, TOX, BARD1, ST8SIA6, CDHR3, SLC16A10, PALM2-AKAP2, ZC2HC1A 
## Negative:  ANK3, NELL2, PITPNC1, RASGRF2, NR3C2, BACH2, ITGA4, PCSK5, THEMIS, MYBL1 
##     PLCB1, UST, SBF2, PELI2, IGF1R, PRKCB, PRKN, RBMS1, EDA, SATB1-AS1 
## PC_ 4 
## Positive:  LINC00299, FRY, RUNX2, ADAM19, MB21D2, MYBL1, ADAM12, PTPN13, PDE4D, KAT2B 
##     MCF2L2, PLCB1, B4GALT5, AUTS2, NTN4, AL136456.1, MSC-AS1, SOS1, DENND3, SASH1 
## Negative:  AL353660.1, MAN2A1, ST8SIA1, BACH1, TOX, KCNQ5, MAML2, FHIT, LEF1, RPLP2 
##     UBASH3B, RPL41, CERS6, GCNT4, IKZF2, LRRC8D, SESN3, TMSB10, GLCCI1, TXK 
## PC_ 5 
## Positive:  JUN, DTL, FOSB, FOS, POLQ, CCNE2, DIAPH3, NCAPG, RRM2, KIF15 
##     MKI67, SPC25, PCNA, WDR62, KIF11, ASPM, CENPU, POC1A, CIT, BUB1B 
## Negative:  CHST11, IL2RA, SLC9A9, ATXN7L1, ST8SIA1, CDHR3, TTN, UBASH3B, AHCYL2, TOX 
##     AF165147.1, JAZF1, SMAD3, LRIG1, GMDS-DT, PHACTR2, ARID5B, GNAO1, CNNM2, SAMD3 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1   0.0786 -12.70        0.76100 1.24e+02  1.24e+02 129.000
## 2      2   0.1530  -8.62        0.83600 6.36e+01  6.36e+01  69.900
## 3      3   0.1250  -4.70        0.97000 3.30e+01  3.29e+01  38.200
## 4      4   0.1990  -4.07        0.87100 1.73e+01  1.72e+01  21.700
## 5      5   0.5640  -6.16        0.90500 9.16e+00  9.05e+00  13.200
## 6      6   0.6960  -5.37        0.84200 4.90e+00  4.78e+00   8.310
## 7      7   0.7780  -4.72        0.81300 2.66e+00  2.55e+00   5.430
## 8      8   0.8650  -4.31        0.84300 1.46e+00  1.37e+00   3.660
## 9      9   0.8980  -3.76        0.87000 8.16e-01  7.47e-01   2.530
## 10    10   0.2460  -5.01        0.04720 4.64e-01  4.10e-01   1.790
## 11    12   0.2570  -4.08        0.05940 1.59e-01  1.27e-01   0.938
## 12    14   0.3250  -5.75        0.13500 5.95e-02  4.00e-02   0.519
## 13    16   0.2200  -3.55        0.02760 2.45e-02  1.31e-02   0.298
## 14    18   0.2150  -3.14        0.01440 1.11e-02  4.33e-03   0.176
## 15    20   0.2070  -2.83       -0.00337 5.42e-03  1.47e-03   0.107
## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
##   0   1   2   3 
## 206  15  12  10
##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 3 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 3 module eigengenes in given set.
## $brown
##  [1] "ZEB2"       "AOAH"       "GNLY"       "AC243829.2" "C1orf21"   
##  [6] "SETBP1"     "KLRD1"      "KLRK1"      "DTHD1"      "TGFBR3"    
## [11] "LINC02384"  "OSBPL5"     "SAMD3"      "TPST2"      "SGCD"      
## [16] "PDGFD"      "SLC4A4"     "AL392086.3" "LYN"        "NCAM1"     
## [21] "FAM49A"     "LGR6"       "JAZF1"      "CEP78"      "TRIO"      
## 
## $blue
##  [1] "DTL"    "POLQ"   "CCNE2"  "DIAPH3" "NCAPG"  "RRM2"   "KIF15"  "MKI67" 
##  [9] "SPC25"  "WDR62"  "POC1A"  "E2F7"  
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "6/10000 permutations failed the Mann-Whitney test."
## $brown
##  [1] "ZEB2"       "AOAH"       "GNLY"       "AC243829.2" "C1orf21"   
##  [6] "SETBP1"     "KLRD1"      "KLRK1"      "DTHD1"      "TGFBR3"    
## [11] "LINC02384"  "OSBPL5"     "SAMD3"      "TPST2"      "SGCD"      
## [16] "PDGFD"      "SLC4A4"     "AL392086.3" "LYN"        "NCAM1"     
## [21] "FAM49A"     "LGR6"       "JAZF1"      "CEP78"      "TRIO"      
## 
## $blue
##  [1] "DTL"    "POLQ"   "CCNE2"  "DIAPH3" "NCAPG"  "RRM2"   "KIF15"  "MKI67" 
##  [9] "SPC25"  "WDR62"  "POC1A"  "E2F7"
saveRDS(mods1, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230601CD4Modules_Treatment_Timepoint.rds")

results.split<-SplitObject(results, "Treatment")

#reduced softpower iteratively until I got three modules
conds<-cbind(c(5,5,6),c(7,8,8))
mods2<-WrapGroupModID(results.split, "NA", conds)
## [1] "Bup.Nalo"
## PC_ 1 
## Positive:  BANK1, ZEB2, AFF3, AOAH, VCAN, IGKC, SLC8A1, AC105402.3, PLXDC2, RPL41 
##     CDK14, HDAC9, IGHM, SETBP1, UBE2E2, RPL13, TRIO, MTRNR2L8, RPLP2, GNLY 
## Negative:  INPP4B, PAG1, CDC14A, ARHGAP15, SERINC5, ANK3, RORA, MDFIC, AKT3, PRKCA 
##     RASGRF2, PDE3B, LEF1, ZBTB20, MBNL1, MGAT5, MAML2, SOS1, RBMS1, NR3C2 
## PC_ 2 
## Positive:  PLCB1, ARHGAP26, ZEB2, AOAH, THEMIS, MYBL1, STAT4, PARP8, C1orf21, TGFBR3 
##     IFNG-AS1, AGAP1, SYTL2, PPP2R2B, SBF2, A2M, IL18RAP, PZP, PDGFD, AUTS2 
## Negative:  TTN, IKZF2, STAM, TSHZ2, AC093865.1, CCDC141, RTKN2, LINC02694, PLCL1, CDHR3 
##     F5, AC013652.1, IL2RA, LDLRAD4, ZC2HC1A, LEF1, MCF2L2, FHIT, TAFA2, TOX 
## PC_ 3 
## Positive:  LINC02694, TOX, IKZF2, NIBAN1, MIR4435-2HG, TGFBR3, AC013652.1, AC093865.1, PPP2R2B, ST8SIA6 
##     C1orf21, ARHGAP26, GTDC1, NCALD, CCDC141, HPGD, PAM, STAM, MSC-AS1, AF165147.1 
## Negative:  PRKCA, NELL2, AC139720.1, TXK, ANK3, MTRNR2L8, CMTM8, BACH2, SERINC5, PCSK5 
##     LEF1, AC233976.1, AC105402.3, NR3C2, RPL13, EDA, IGF1R, BCL2, PRKN, RPLP2 
## PC_ 4 
## Positive:  TNFAIP3, IFNG-AS1, ANK3, IL18RAP, LRIG1, XIST, IL12RB2, FMN1, MCOLN2, IL32 
##     IL18R1, LINC01934, A2M, ITGA4, INPP4B, CNOT6L, LTB, FKBP5, RNF19A, AF165147.1 
## Negative:  BANK1, AFF3, SLC8A1, PLXDC2, GRK3, VCAN, UBE2E2, CDK14, HDAC9, MTSS1 
##     TRIO, BACH2, ZEB2, CCSER1, TCF7L2, MAML3, CTBP2, IGHM, ALOX5, TCF4 
## PC_ 5 
## Positive:  ST8SIA1, ITGA4, SESN3, LINC01934, AL353660.1, TOX, AOAH, APBA2, TRPS1, TXK 
##     C12orf42, GCNT4, LEF1, MAML2, SGPP2, CERS6, LRRC8D, KCNQ5, SLC9A9, DTHD1 
## Negative:  ADAM12, FRY, RUNX2, CCR6, LINC00299, PTPN13, PLCB1, PLD1, AL136456.1, MTRNR2L8 
##     AC105402.3, LINC02694, B4GALT5, MB21D2, AL589693.1, RBMS1, PDE4D, ADAM23, CFH, AC013652.1 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1  0.00922  3.310         0.9520 84.40000  8.44e+01 88.4000
## 2      2  0.02700  3.110         0.9570 43.30000  4.31e+01 47.7000
## 3      3  0.00795  1.120         0.8960 22.40000  2.22e+01 26.0000
## 4      4  0.00748 -0.913         0.7570 11.70000  1.15e+01 14.4000
## 5      5  0.01410 -0.915         0.7810  6.13000  6.02e+00  8.0800
## 6      6  0.05210 -1.560         0.6150  3.25000  3.16e+00  4.6500
## 7      7  0.28100 -3.150         0.4940  1.74000  1.69e+00  2.7100
## 8      8  0.64200 -3.690         0.7450  0.94200  8.97e-01  1.6000
## 9      9  0.81200 -3.760         0.8580  0.51500  4.91e-01  0.9580
## 10    10  0.91100 -3.620         0.9210  0.28400  2.67e-01  0.5790
## 11    12  0.85800 -2.840         0.8300  0.08990  8.06e-02  0.2180
## 12    14  0.87100 -2.240         0.8360  0.03000  2.55e-02  0.0927
## 13    16  0.90900 -2.090         0.8850  0.01060  8.37e-03  0.0472
## 14    18  0.24700 -3.550         0.0388  0.00401  2.77e-03  0.0267
## 15    20  0.32000 -4.480         0.1960  0.00163  9.11e-04  0.0159
## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
##   0   1   2   3   4 
## 112  17  14  14  10
##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
## $blue
##  [1] "BANK1"  "AFF3"   "VCAN"   "IGKC"   "SLC8A1" "PLXDC2" "CDK14"  "HDAC9" 
##  [9] "IGHM"   "SETBP1" "UBE2E2" "TRIO"   "GRK3"   "TCF4"  
## 
## $yellow
##  [1] "ZEB2"       "AOAH"       "ARHGAP26"   "C1orf21"    "TGFBR3"    
##  [6] "AGAP1"      "PPP2R2B"    "PDGFD"      "DTHD1"      "AC243829.2"
## 
## $turquoise
##  [1] "INPP4B"     "PAG1"       "CDC14A"     "ARHGAP15"   "SERINC5"   
##  [6] "ANK3"       "MDFIC"      "PRKCA"      "RASGRF2"    "PDE3B"     
## [11] "MGAT5"      "MAML2"      "NR3C2"      "AC139720.1" "NELL2"     
## [16] "BCL2"       "PRKN"      
## 
## $brown
##  [1] "TTN"        "IKZF2"      "STAM"       "AC093865.1" "CCDC141"   
##  [6] "RTKN2"      "LINC02694"  "CDHR3"      "AC013652.1" "IL2RA"     
## [11] "TOX"        "ATXN7L1"    "ST8SIA6"    "HPGD"      
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $blue
##  [1] "BANK1"  "AFF3"   "VCAN"   "IGKC"   "SLC8A1" "PLXDC2" "CDK14"  "HDAC9" 
##  [9] "IGHM"   "SETBP1" "UBE2E2" "TRIO"   "GRK3"   "TCF4"  
## 
## $yellow
##  [1] "ZEB2"       "AOAH"       "ARHGAP26"   "C1orf21"    "TGFBR3"    
##  [6] "AGAP1"      "PPP2R2B"    "PDGFD"      "DTHD1"      "AC243829.2"
## 
## $turquoise
##  [1] "INPP4B"     "PAG1"       "CDC14A"     "ARHGAP15"   "SERINC5"   
##  [6] "ANK3"       "MDFIC"      "PRKCA"      "RASGRF2"    "PDE3B"     
## [11] "MGAT5"      "MAML2"      "NR3C2"      "AC139720.1" "NELL2"     
## [16] "BCL2"       "PRKN"      
## 
## $brown
##  [1] "TTN"        "IKZF2"      "STAM"       "AC093865.1" "CCDC141"   
##  [6] "RTKN2"      "LINC02694"  "CDHR3"      "AC013652.1" "IL2RA"     
## [11] "TOX"        "ATXN7L1"    "ST8SIA6"    "HPGD"      
## 
## [1] "Naltrexone"
## PC_ 1 
## Positive:  INPP4B, PRKCA, LEF1, ANK3, TSHZ2, PAG1, BCL2, CMTM8, PLCL1, CDC14A 
##     RPL13, BACH2, XIST, FAAH2, RPLP2, NELL2, RPS18, MAP3K1, AC139720.1, AL589693.1 
## Negative:  ZEB2, C1orf21, AOAH, SYNE1, GNLY, SETBP1, TGFBR3, LINC02384, SAMD3, OSBPL5 
##     PDGFD, ARHGAP26, PPP2R2B, KLRD1, AGAP1, ADGRG5, AC243829.2, KLRK1, LYN, SYTL3 
## PC_ 2 
## Positive:  MTRNR2L8, RPL13, RPLP2, RPLP1, RPL41, RPS18, RPS28, RPS23, RPS19, RPS12 
##     RPS2, FOS, JUN, FOSB, JUNB, IER2, AC022217.3, AL691403.1, EGR1, AC105402.3 
## Negative:  ARHGAP15, RORA, MBNL1, PAG1, CDC14A, INPP4B, MGAT5, RBMS1, MDFIC, PARP8 
##     RABGAP1L, FRY, RUNX2, ADAM19, PPP3CA, THEMIS, MAP3K1, ANK3, CBLB, SMYD3 
## PC_ 3 
## Positive:  LINC02694, TTN, ENTPD1, CCDC141, STAM, AC013652.1, RTKN2, IL2RA, IKZF2, AC093865.1 
##     DUSP4, HPGD, NIBAN1, TOX, MCF2L2, ZC2HC1A, PALM2-AKAP2, F5, MIR181A1HG, CDHR3 
## Negative:  BACH2, NELL2, RASGRF2, PLCB1, IGF1R, NR3C2, RPL41, PCSK5, RPS2, RPS12 
##     RPS23, RPL13, RPLP2, ANK3, RPS19, RPS18, RPS28, TAFA1, RPLP1, SBF2 
## PC_ 4 
## Positive:  FRY, PTPN13, ADAM19, ADAM12, PDE4D, PLCB1, BTBD11, MYBL1, LINC00299, MB21D2 
##     ALOX5, RORA, AC105402.3, TANC1, AL589693.1, BCL2, MTRNR2L8, AL136456.1, PTPRM, AUTS2 
## Negative:  RPS2, FOSB, RPS28, RPL41, RPS23, JUN, FOS, RPLP1, RPS12, RPLP2 
##     RPS19, RPL13, RPS18, JUNB, AC022217.3, IKZF2, IER2, AC093865.1, PLCG2, DNAJA1 
## PC_ 5 
## Positive:  JUN, PDE4D, FOSB, FOS, DNAJA1, ADAM12, JUNB, FRY, AC022217.3, LINC00299 
##     RPL41, RPS19, RPS2, IER2, RPS12, AL136456.1, RPLP1, RPS28, RPS23, NAMPT 
## Negative:  UBASH3B, LEF1, AL353660.1, ST8SIA1, AC139720.1, TSHZ2, SESN3, AC233976.1, CMTM8, GCNT4 
##     ATXN7L1, FAAH2, GRK5, IFNG-AS1, MAML2, CERS6, FHIT, AOAH, SLC9A9, FMN1 
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1 0.187000 58.600        0.05800 79.9000  79.60000 84.700
## 2      2 0.174000 28.100        0.03250 41.4000  41.30000 46.700
## 3      3 0.054100  2.730        0.64000 21.8000  21.60000 26.200
## 4      4 0.003750  0.525        0.78200 11.6000  11.50000 14.900
## 5      5 0.000215 -0.084        0.73000  6.2800   6.19000  8.590
## 6      6 0.134000 -1.480        0.59800  3.4700   3.37000  5.260
## 7      7 0.446000 -2.320        0.66400  1.9500   1.86000  3.480
## 8      8 0.531000 -2.130        0.46200  1.1200   1.03000  2.360
## 9      9 0.575000 -2.250        0.46200  0.6600   0.57300  1.640
## 10    10 0.630000 -1.880        0.60800  0.3980   0.32300  1.210
## 11    12 0.064900 -2.020       -0.00604  0.1570   0.10700  0.711
## 12    14 0.031000 -1.540        0.14200  0.0694   0.03620  0.438
## 13    16 0.037900 -1.140        0.03000  0.0338   0.01250  0.276
## 14    18 0.043800 -1.100        0.01880  0.0178   0.00441  0.176
## 15    20 0.655000 -1.040        0.76800  0.0100   0.00168  0.113
## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
##   0   1   2   3 
## 102  23  22  10
##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $brown
##  [1] "INPP4B"   "PRKCA"    "ANK3"     "PAG1"     "BCL2"     "CDC14A"  
##  [7] "MAP3K1"   "ARHGAP15" "ADAM19"   "ETV6"    
## 
## $blue
##  [1] "RPL13"      "RPLP2"      "RPS18"      "RPLP1"      "RPS23"     
##  [6] "RPL41"      "RPS28"      "RPS19"      "RPS12"      "RPS2"      
## [11] "FOS"        "JUN"        "FOSB"       "JUNB"       "IER2"      
## [16] "AC022217.3" "AL691403.1" "EGR1"       "EIF4A3"     "TEX14"     
## [21] "CSKMT"      "DNAJA1"    
## 
## $turquoise
##  [1] "ZEB2"       "C1orf21"    "AOAH"       "SYNE1"      "GNLY"      
##  [6] "SETBP1"     "TGFBR3"     "LINC02384"  "SAMD3"      "OSBPL5"    
## [11] "PDGFD"      "ARHGAP26"   "PPP2R2B"    "KLRD1"      "AGAP1"     
## [16] "ADGRG5"     "AC243829.2" "KLRK1"      "LYN"        "SYTL3"     
## [21] "PRSS23"     "MCTP2"      "VAV3"      
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $brown
##  [1] "INPP4B"   "PRKCA"    "ANK3"     "PAG1"     "BCL2"     "CDC14A"  
##  [7] "MAP3K1"   "ARHGAP15" "ADAM19"   "ETV6"    
## 
## $blue
##  [1] "RPL13"      "RPLP2"      "RPS18"      "RPLP1"      "RPS23"     
##  [6] "RPL41"      "RPS28"      "RPS19"      "RPS12"      "RPS2"      
## [11] "FOS"        "JUN"        "FOSB"       "JUNB"       "IER2"      
## [16] "AC022217.3" "AL691403.1" "EGR1"       "EIF4A3"     "TEX14"     
## [21] "CSKMT"      "DNAJA1"    
## 
## $turquoise
##  [1] "ZEB2"       "C1orf21"    "AOAH"       "SYNE1"      "GNLY"      
##  [6] "SETBP1"     "TGFBR3"     "LINC02384"  "SAMD3"      "OSBPL5"    
## [11] "PDGFD"      "ARHGAP26"   "PPP2R2B"    "KLRD1"      "AGAP1"     
## [16] "ADGRG5"     "AC243829.2" "KLRK1"      "LYN"        "SYTL3"     
## [21] "PRSS23"     "MCTP2"      "VAV3"      
## 
## [1] "Methadone"
## PC_ 1 
## Positive:  INPP4B, CAMK4, PRKCA, ANK3, LEF1, ARHGAP15, CDC14A, MGAT5, HIVEP2, GNAQ 
##     TSHZ2, NR3C2, FAAH2, BCL2, MAML2, AC139720.1, NELL2, PDE3B, BACH2, DOCK10 
## Negative:  ZEB2, AOAH, GNLY, AC243829.2, C1orf21, SETBP1, KLRD1, KLRK1, SYNE1, OSBPL5 
##     PDGFD, LINC02384, DTHD1, LYN, TGFBR3, SAMD3, ADGRG5, SGCD, SLC4A4, AL392086.3 
## PC_ 2 
## Positive:  RPLP2, RPL41, RPS27, RPS2, FOS, JUN, FOSB, AC022217.3, TUBA1A, PLXNA4 
##     IER2, CLNK, FHIT, TSHZ2, SH3RF3, PRKCA, AL589693.1, EGR1, FMN1, SDK2 
## Negative:  RABGAP1L, SAMD3, MBNL1, TGFBR3, CBLB, ZEB2, JAZF1, ARHGAP15, PAM, ARHGAP26 
##     RORA, DPYD, NCALD, MCTP2, SYNE1, AOAH, GTDC1, DLEU2, ST8SIA4, PPP2R2B 
## PC_ 3 
## Positive:  ANK3, NR3C2, NELL2, MYBL1, PLCB1, RASGRF2, MCTP2, TAFA1, ITGA4, BACH2 
##     SBF2, AOAH, UST, PCSK5, PELI2, ZEB2, PRKN, KLRD1, GNLY, KLRK1 
## Negative:  LINC02694, TTN, AC013652.1, CCDC141, STAM, MIR181A1HG, DIAPH3, NCAPG, ASPM, BARD1 
##     KNL1, IKZF2, RTKN2, MKI67, DUSP4, TOP2A, RRM2, F5, BUB1B, KIF15 
## PC_ 4 
## Positive:  LINC02694, STAM, TTN, IKZF2, CCDC141, IL2RA, AC093865.1, AC013652.1, FANK1, CDHR3 
##     TOX, ATXN7L1, HACD1, RTKN2, CTLA4, IL7, SNED1, HPGD, MCF2L2, F5 
## Negative:  DIAPH3, KIF15, RRM2, BUB1B, ASPM, E2F7, POLQ, KIF18B, CDCA2, MKI67 
##     DEPDC1B, DTL, KIFC1, NCAPG, CDC25C, ANLN, TOP2A, PCLAF, CENPU, SPC25 
## PC_ 5 
## Positive:  AL353660.1, TXK, IKZF2, KCNQ5, TOX, AC093865.1, SESN3, GCNT4, LEF1, BACH1 
##     CERS6, VAV3, UBASH3B, ST8SIA1, AC233976.1, ATXN7L1, FHIT, GLCCI1, MAML2, CDHR3 
## Negative:  FRY, LINC00299, PTPN13, RUNX2, MB21D2, ADAM12, AUTS2, PLCB1, MSC-AS1, RBMS1 
##     PDE4D, B4GALT5, MCF2L2, RORA, MYBL1, AFDN, PLD1, SASH1, HLF, SYTL2 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.   max.k.
## 1      1    0.113 -17.00         0.6740 1.10e+02  1.09e+02 115.0000
## 2      2    0.172  -8.89         0.7740 5.65e+01  5.63e+01  62.5000
## 3      3    0.194  -6.16         0.8820 2.94e+01  2.93e+01  34.5000
## 4      4    0.124  -3.41         0.9400 1.55e+01  1.53e+01  19.2000
## 5      5    0.119  -2.25         0.7460 8.21e+00  8.09e+00  10.9000
## 6      6    0.339  -3.06         0.7980 4.41e+00  4.33e+00   6.6900
## 7      7    0.603  -3.93         0.7860 2.40e+00  2.33e+00   4.3100
## 8      8    0.781  -3.69         0.8860 1.33e+00  1.25e+00   2.8600
## 9      9    0.191  -5.53        -0.0315 7.48e-01  6.78e-01   1.9500
## 10    10    0.209  -4.93        -0.0108 4.28e-01  3.75e-01   1.3600
## 11    12    0.326  -6.47         0.1450 1.49e-01  1.15e-01   0.6930
## 12    14    0.317  -6.04         0.1220 5.65e-02  3.54e-02   0.3690
## 13    16    0.267  -4.19         0.0642 2.33e-02  1.18e-02   0.2020
## 14    18    0.260  -3.71         0.0629 1.04e-02  3.98e-03   0.1130
## 15    20    0.314  -4.31         0.1590 4.98e-03  1.38e-03   0.0645
## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
##   0   1   2   3   4 
## 150  27  13  13  12
##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $blue
##  [1] "INPP4B"  "CAMK4"   "PRKCA"   "ANK3"    "LEF1"    "MGAT5"   "HIVEP2" 
##  [8] "NR3C2"   "MAML2"   "NELL2"   "PDE3B"   "BACH2"   "RASGRF2"
## 
## $turquoise
##  [1] "ZEB2"       "AOAH"       "GNLY"       "AC243829.2" "C1orf21"   
##  [6] "SETBP1"     "KLRD1"      "KLRK1"      "SYNE1"      "OSBPL5"    
## [11] "PDGFD"      "LINC02384"  "DTHD1"      "LYN"        "TGFBR3"    
## [16] "SAMD3"      "ADGRG5"     "SGCD"       "SLC4A4"     "AL392086.3"
## [21] "ARHGAP26"   "NCAM1"      "PPP2R2B"    "KLRF1"      "FAM49A"    
## [26] "JAZF1"      "MCTP2"     
## 
## $brown
##  [1] "DIAPH3"  "NCAPG"   "ASPM"    "MKI67"   "TOP2A"   "RRM2"    "BUB1B"  
##  [8] "KIF15"   "CDCA2"   "E2F7"    "POLQ"    "KIF18B"  "DEPDC1B" "DTL"    
## [15] "KIFC1"   "CDC25C"  "ANLN"    "PCLAF"   "CENPU"   "SPC25"   "PBK"    
## [22] "ECT2"    "POC1A"   "CIT"     "CDK1"   
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1/10000 permutations failed the Mann-Whitney test."
## $blue
##  [1] "INPP4B"  "CAMK4"   "PRKCA"   "ANK3"    "LEF1"    "MGAT5"   "HIVEP2" 
##  [8] "NR3C2"   "MAML2"   "NELL2"   "PDE3B"   "BACH2"   "RASGRF2"
## 
## $turquoise
##  [1] "ZEB2"       "AOAH"       "GNLY"       "AC243829.2" "C1orf21"   
##  [6] "SETBP1"     "KLRD1"      "KLRK1"      "SYNE1"      "OSBPL5"    
## [11] "PDGFD"      "LINC02384"  "DTHD1"      "LYN"        "TGFBR3"    
## [16] "SAMD3"      "ADGRG5"     "SGCD"       "SLC4A4"     "AL392086.3"
## [21] "ARHGAP26"   "NCAM1"      "PPP2R2B"    "KLRF1"      "FAM49A"    
## [26] "JAZF1"      "MCTP2"     
## 
## $brown
##  [1] "DIAPH3"  "NCAPG"   "ASPM"    "MKI67"   "TOP2A"   "RRM2"    "BUB1B"  
##  [8] "KIF15"   "CDCA2"   "E2F7"    "POLQ"    "KIF18B"  "DEPDC1B" "DTL"    
## [15] "KIFC1"   "CDC25C"  "ANLN"    "PCLAF"   "CENPU"   "SPC25"   "PBK"    
## [22] "ECT2"    "POC1A"   "CIT"     "CDK1"
saveRDS(mods2, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230601CD4Modules_Treatment.rds")

#reduced softpower iteratively until I got three modules
mods3<-ModID(results, nPCS = 8, softpower = 7)
## PC_ 1 
## Positive:  ZEB2, AOAH, LYN, BANK1, GNLY, SETBP1, C1orf21, AC105402.3, AFF3, AC243829.2 
##     MTRNR2L8, CCL5, VCAN, KLRD1, EBF1, IGKC, SLC8A1, KLRK1, HDAC9, PDGFD 
## Negative:  INPP4B, PAG1, ARHGAP15, CDC14A, ANK3, PRKCA, LEF1, RORA, MGAT5, GPRIN3 
##     MDFIC, BCL2, ADAM19, MAP3K1, GNAQ, MAML2, RBMS1, MBNL1, NR3C2, PDE3B 
## PC_ 2 
## Positive:  ZEB2, C1orf21, TGFBR3, ARHGAP26, PPP2R2B, MCTP2, AOAH, NCALD, PARP8, SYTL2 
##     LINC02384, PDGFD, MYBL1, AGAP1, GNLY, AC243829.2, MVB12B, PLCB1, KLRD1, OSBPL5 
## Negative:  RPL13, RPLP2, RPL41, TSHZ2, LEF1, PRKCA, JUNB, CMTM8, FHIT, FOS 
##     JUN, PLCL1, MTRNR2L8, SESN3, FOSB, TXK, AL109930.1, XIST, AC233976.1, AL353660.1 
## PC_ 3 
## Positive:  ANK3, BACH2, NELL2, NR3C2, RASGRF2, PLCB1, SBF2, PCSK5, PELI2, PRKN 
##     THEMIS, IGF1R, TAFA1, MYBL1, RBMS1, UST, DPP4, PRKCA, EDA, BTBD11 
## Negative:  LINC02694, IKZF2, TTN, AC093865.1, CCDC141, STAM, AC013652.1, TOX, RTKN2, CDHR3 
##     DUSP4, IL2RA, F5, HPGD, MIR181A1HG, ZC2HC1A, ATXN7L1, ST8SIA6, ENTPD1, NIBAN1 
## PC_ 4 
## Positive:  RORA, MYBL1, IL18RAP, SYTL2, TNFAIP3, LINC00299, TGFBR3, AGAP1, PPP2R2B, THEMIS 
##     HIVEP3, MCOLN2, LRIG1, NCALD, PTPRM, TPRG1, ANK3, C1orf21, NIBAN1, AGPAT4 
## Negative:  BANK1, AFF3, LYN, SLC8A1, PLXDC2, VCAN, GRK3, EBF1, UBE2E2, CDK14 
##     HDAC9, TRIO, IGKC, IGHM, BACH2, CCSER1, TCF4, MTSS1, EVI5, SOX5 
## PC_ 5 
## Positive:  FRY, ADAM12, PDE4D, PTPN13, LINC00299, ADAM19, RUNX2, CCR6, PLCB1, MB21D2 
##     AL136456.1, MCF2L2, AUTS2, B4GALT5, GAB2, RBMS1, AFDN, ELOVL4, SOS1, AL589693.1 
## Negative:  AL353660.1, LEF1, ST8SIA1, SESN3, TXK, GCNT4, TOX, LINC01934, MAML2, MLLT3 
##     UBASH3B, AC233976.1, ATXN7L1, AC243829.2, IKZF2, AOAH, ITGA4, FHIT, AC093865.1, GLCCI1 
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.   max.k.
## 1      1  0.06620 15.800         0.6980 1.20e+02  1.20e+02 125.0000
## 2      2  0.02950  5.240         0.6450 6.14e+01  6.12e+01  67.0000
## 3      3  0.00232  0.932         0.7240 3.15e+01  3.13e+01  36.2000
## 4      4  0.00012 -0.154         0.7550 1.63e+01  1.61e+01  19.8000
## 5      5  0.00433 -0.726         0.6530 8.46e+00  8.34e+00  10.9000
## 6      6  0.02980 -1.530         0.6920 4.43e+00  4.34e+00   6.1100
## 7      7  0.04440 -1.470         0.6740 2.33e+00  2.27e+00   3.4600
## 8      8  0.15200 -8.450         0.1180 1.24e+00  1.19e+00   2.0200
## 9      9  0.58000 -3.770         0.7500 6.65e-01  6.34e-01   1.2300
## 10    10  0.25500 -8.520         0.0431 3.61e-01  3.37e-01   0.7680
## 11    12  0.34500 -7.550         0.2160 1.10e-01  9.92e-02   0.3120
## 12    14  0.33600 -5.830         0.2060 3.52e-02  2.95e-02   0.1340
## 13    16  0.30500 -4.570         0.1590 1.21e-02  8.83e-03   0.0599
## 14    18  0.79000 -1.820         0.7950 4.46e-03  2.80e-03   0.0278
## 15    20  0.82600 -1.590         0.8420 1.79e-03  9.09e-04   0.0158
## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
##   0   1   2   3   4 
## 188  14  14  11  11
##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
## $blue
##  [1] "LYN"    "BANK1"  "AFF3"   "VCAN"   "EBF1"   "IGKC"   "SLC8A1" "HDAC9" 
##  [9] "PLXDC2" "CDK14"  "IGHM"   "GRK3"   "UBE2E2" "TRIO"  
## 
## $turquoise
##  [1] "INPP4B"     "PAG1"       "ARHGAP15"   "CDC14A"     "ANK3"      
##  [6] "PRKCA"      "LEF1"       "MDFIC"      "BCL2"       "MAML2"     
## [11] "NR3C2"      "RASGRF2"    "AC139720.1" "NELL2"     
## 
## $brown
##  [1] "LINC02694"  "IKZF2"      "TTN"        "AC093865.1" "CCDC141"   
##  [6] "STAM"       "AC013652.1" "RTKN2"      "IL2RA"      "HPGD"      
## [11] "FANK1"     
## 
## $yellow
##  [1] "TOP2A"  "MKI67"  "ASPM"   "NCAPG"  "KIF15"  "CENPF"  "ANLN"   "KIF18B"
##  [9] "DLGAP5" "CDCA2"  "KIF14" 
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "11/10000 permutations failed the Mann-Whitney test."
## $blue
##  [1] "LYN"    "BANK1"  "AFF3"   "VCAN"   "EBF1"   "IGKC"   "SLC8A1" "HDAC9" 
##  [9] "PLXDC2" "CDK14"  "IGHM"   "GRK3"   "UBE2E2" "TRIO"  
## 
## $turquoise
##  [1] "INPP4B"     "PAG1"       "ARHGAP15"   "CDC14A"     "ANK3"      
##  [6] "PRKCA"      "LEF1"       "MDFIC"      "BCL2"       "MAML2"     
## [11] "NR3C2"      "RASGRF2"    "AC139720.1" "NELL2"     
## 
## $brown
##  [1] "LINC02694"  "IKZF2"      "TTN"        "AC093865.1" "CCDC141"   
##  [6] "STAM"       "AC013652.1" "RTKN2"      "IL2RA"      "HPGD"      
## [11] "FANK1"     
## 
## $yellow
##  [1] "TOP2A"  "MKI67"  "ASPM"   "NCAPG"  "KIF15"  "CENPF"  "ANLN"   "KIF18B"
##  [9] "DLGAP5" "CDCA2"  "KIF14"
saveRDS(mods3, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230601CD4Modules.rds")
devtools::session_info()
## Warning in system("timedatectl", intern = TRUE): running command 'timedatectl'
## had status 1
## - Session info ---------------------------------------------------------------
##  setting  value
##  version  R version 4.2.0 (2022-04-22)
##  os       Red Hat Enterprise Linux 8.7 (Ootpa)
##  system   x86_64, linux-gnu
##  ui       X11
##  language (EN)
##  collate  C
##  ctype    C
##  tz       Etc/UTC
##  date     2023-06-01
##  pandoc   2.17.1.1 @ /usr/lib/rstudio-server/bin/quarto/bin/ (via rmarkdown)
## 
## - Packages -------------------------------------------------------------------
##  package          * version   date (UTC) lib source
##  abind              1.4-5     2016-07-21 [2] CRAN (R 4.2.0)
##  AnnotationDbi      1.60.2    2023-03-10 [1] Bioconductor
##  backports          1.4.1     2021-12-13 [2] CRAN (R 4.2.0)
##  base64enc          0.1-3     2015-07-28 [2] CRAN (R 4.2.0)
##  Biobase            2.58.0    2022-11-01 [1] Bioconductor
##  BiocGenerics       0.44.0    2022-11-01 [1] Bioconductor
##  BiocParallel       1.32.6    2023-03-17 [1] Bioconductor
##  Biostrings         2.66.0    2022-11-01 [1] Bioconductor
##  bit                4.0.5     2022-11-15 [2] CRAN (R 4.2.0)
##  bit64              4.0.5     2020-08-30 [2] CRAN (R 4.2.0)
##  bitops             1.0-7     2021-04-24 [2] CRAN (R 4.2.0)
##  blob               1.2.4     2023-03-17 [1] CRAN (R 4.2.0)
##  bslib              0.4.2     2022-12-16 [1] CRAN (R 4.2.0)
##  cachem             1.0.8     2023-05-01 [1] CRAN (R 4.2.0)
##  callr              3.7.3     2022-11-02 [1] CRAN (R 4.2.0)
##  checkmate          2.1.0     2022-04-21 [2] CRAN (R 4.2.0)
##  cli                3.6.1     2023-03-23 [1] CRAN (R 4.2.0)
##  cluster            2.1.4     2022-08-22 [2] CRAN (R 4.2.0)
##  codetools          0.2-19    2023-02-01 [2] CRAN (R 4.2.0)
##  colorspace         2.1-0     2023-01-23 [2] CRAN (R 4.2.0)
##  cowplot          * 1.1.1     2020-12-30 [2] CRAN (R 4.2.0)
##  crayon             1.5.2     2022-09-29 [2] CRAN (R 4.2.0)
##  data.table         1.14.8    2023-02-17 [2] CRAN (R 4.2.0)
##  DBI                1.1.3     2022-06-18 [2] CRAN (R 4.2.0)
##  deldir             1.0-6     2021-10-23 [2] CRAN (R 4.2.0)
##  devtools           2.4.5     2022-10-11 [1] CRAN (R 4.2.0)
##  digest             0.6.31    2022-12-11 [2] CRAN (R 4.2.0)
##  doParallel       * 1.0.17    2022-02-07 [1] CRAN (R 4.2.0)
##  dplyr            * 1.1.2     2023-04-20 [1] CRAN (R 4.2.0)
##  dynamicTreeCut   * 1.63-1    2016-03-11 [2] CRAN (R 4.2.0)
##  ellipsis           0.3.2     2021-04-29 [2] CRAN (R 4.2.0)
##  evaluate           0.20      2023-01-17 [2] CRAN (R 4.2.0)
##  fansi              1.0.4     2023-01-22 [2] CRAN (R 4.2.0)
##  fastcluster      * 1.2.3     2021-05-24 [2] CRAN (R 4.2.0)
##  fastmap            1.1.1     2023-02-24 [1] CRAN (R 4.2.0)
##  fastmatch          1.1-3     2021-07-23 [2] CRAN (R 4.2.0)
##  fitdistrplus       1.1-8     2022-03-10 [2] CRAN (R 4.2.0)
##  flashClust       * 1.01-2    2012-08-21 [1] CRAN (R 4.2.0)
##  foreach          * 1.5.2     2022-02-02 [2] CRAN (R 4.2.0)
##  foreign            0.8-84    2022-12-06 [2] CRAN (R 4.2.0)
##  Formula            1.2-5     2023-02-24 [1] CRAN (R 4.2.0)
##  fs                 1.6.1     2023-02-06 [2] CRAN (R 4.2.0)
##  future             1.32.0    2023-03-07 [1] CRAN (R 4.2.0)
##  future.apply       1.10.0    2022-11-05 [1] CRAN (R 4.2.0)
##  generics           0.1.3     2022-07-05 [2] CRAN (R 4.2.0)
##  GenomeInfoDb       1.34.9    2023-02-02 [1] Bioconductor
##  GenomeInfoDbData   1.2.9     2023-03-17 [1] Bioconductor
##  GenomicRanges      1.50.2    2022-12-16 [1] Bioconductor
##  ggplot2          * 3.4.2     2023-04-03 [1] CRAN (R 4.2.0)
##  ggrepel            0.9.3     2023-02-03 [1] CRAN (R 4.2.0)
##  ggridges           0.5.4     2022-09-26 [1] CRAN (R 4.2.0)
##  globals            0.16.2    2022-11-21 [1] CRAN (R 4.2.0)
##  glue               1.6.2     2022-02-24 [2] CRAN (R 4.2.0)
##  GO.db              3.16.0    2023-03-17 [1] Bioconductor
##  goftest            1.2-3     2021-10-07 [2] CRAN (R 4.2.0)
##  gridExtra          2.3       2017-09-09 [2] CRAN (R 4.2.0)
##  gtable             0.3.3     2023-03-21 [1] CRAN (R 4.2.0)
##  highr              0.10      2022-12-22 [1] CRAN (R 4.2.0)
##  Hmisc            * 5.1-0     2023-05-08 [1] CRAN (R 4.2.0)
##  htmlTable          2.4.1     2022-07-07 [1] CRAN (R 4.2.0)
##  htmltools          0.5.5     2023-03-23 [1] CRAN (R 4.2.0)
##  htmlwidgets        1.6.2     2023-03-17 [1] CRAN (R 4.2.0)
##  httpuv             1.6.9     2023-02-14 [1] CRAN (R 4.2.0)
##  httr               1.4.5     2023-02-24 [1] CRAN (R 4.2.0)
##  ica                1.0-3     2022-07-08 [2] CRAN (R 4.2.0)
##  igraph             1.4.2     2023-04-07 [1] CRAN (R 4.2.0)
##  impute             1.72.3    2023-01-19 [1] Bioconductor
##  IRanges            2.32.0    2022-11-01 [1] Bioconductor
##  irlba              2.3.5.1   2022-10-03 [1] CRAN (R 4.2.0)
##  iterators        * 1.0.14    2022-02-05 [2] CRAN (R 4.2.0)
##  jquerylib          0.1.4     2021-04-26 [2] CRAN (R 4.2.0)
##  jsonlite           1.8.4     2022-12-06 [2] CRAN (R 4.2.0)
##  KEGGREST           1.38.0    2022-11-01 [1] Bioconductor
##  KernSmooth         2.23-20   2021-05-03 [2] CRAN (R 4.2.0)
##  knitr              1.42      2023-01-25 [1] CRAN (R 4.2.0)
##  later              1.3.0     2021-08-18 [2] CRAN (R 4.2.0)
##  lattice            0.21-8    2023-04-05 [1] CRAN (R 4.2.0)
##  lazyeval           0.2.2     2019-03-15 [2] CRAN (R 4.2.0)
##  leiden             0.4.3     2022-09-10 [1] CRAN (R 4.2.0)
##  lifecycle          1.0.3     2022-10-07 [1] CRAN (R 4.2.0)
##  listenv            0.9.0     2022-12-16 [2] CRAN (R 4.2.0)
##  lmtest             0.9-40    2022-03-21 [2] CRAN (R 4.2.0)
##  magrittr           2.0.3     2022-03-30 [2] CRAN (R 4.2.0)
##  MASS               7.3-59    2023-04-21 [1] CRAN (R 4.2.0)
##  Matrix             1.5-4     2023-04-04 [1] CRAN (R 4.2.0)
##  matrixStats        0.63.0    2022-11-18 [2] CRAN (R 4.2.0)
##  memoise            2.0.1     2021-11-26 [2] CRAN (R 4.2.0)
##  mime               0.12      2021-09-28 [2] CRAN (R 4.2.0)
##  miniUI             0.1.1.1   2018-05-18 [2] CRAN (R 4.2.0)
##  munsell            0.5.0     2018-06-12 [2] CRAN (R 4.2.0)
##  nlme               3.1-162   2023-01-31 [1] CRAN (R 4.2.0)
##  nnet               7.3-19    2023-05-03 [1] CRAN (R 4.2.0)
##  openxlsx         * 4.2.5.2   2023-02-06 [1] CRAN (R 4.2.0)
##  parallelly         1.35.0    2023-03-23 [1] CRAN (R 4.2.0)
##  patchwork          1.1.2     2022-08-19 [1] CRAN (R 4.2.0)
##  pbapply            1.7-0     2023-01-13 [1] CRAN (R 4.2.0)
##  pillar             1.9.0     2023-03-22 [1] CRAN (R 4.2.0)
##  pkgbuild           1.4.0     2022-11-27 [1] CRAN (R 4.2.0)
##  pkgconfig          2.0.3     2019-09-22 [2] CRAN (R 4.2.0)
##  pkgload            1.3.2     2022-11-16 [1] CRAN (R 4.2.0)
##  plotly             4.10.1    2022-11-07 [1] CRAN (R 4.2.0)
##  plyr               1.8.8     2022-11-11 [1] CRAN (R 4.2.0)
##  png                0.1-8     2022-11-29 [1] CRAN (R 4.2.0)
##  polyclip           1.10-4    2022-10-20 [1] CRAN (R 4.2.0)
##  preprocessCore     1.60.2    2023-01-19 [1] Bioconductor
##  prettyunits        1.1.1     2020-01-24 [2] CRAN (R 4.2.0)
##  processx           3.8.1     2023-04-18 [1] CRAN (R 4.2.0)
##  profvis            0.3.8     2023-05-02 [1] CRAN (R 4.2.0)
##  progressr          0.13.0    2023-01-10 [1] CRAN (R 4.2.0)
##  promises           1.2.0.1   2021-02-11 [2] CRAN (R 4.2.0)
##  ps                 1.7.5     2023-04-18 [1] CRAN (R 4.2.0)
##  purrr              1.0.1     2023-01-10 [1] CRAN (R 4.2.0)
##  R6                 2.5.1     2021-08-19 [2] CRAN (R 4.2.0)
##  RANN               2.6.1     2019-01-08 [2] CRAN (R 4.2.0)
##  RColorBrewer       1.1-3     2022-04-03 [2] CRAN (R 4.2.0)
##  Rcpp               1.0.10    2023-01-22 [1] CRAN (R 4.2.0)
##  RcppAnnoy          0.0.20    2022-10-27 [1] CRAN (R 4.2.0)
##  RcppRoll           0.3.0     2018-06-05 [2] CRAN (R 4.2.0)
##  RCurl              1.98-1.12 2023-03-27 [1] CRAN (R 4.2.0)
##  remotes            2.4.2     2021-11-30 [2] CRAN (R 4.2.0)
##  reshape2           1.4.4     2020-04-09 [2] CRAN (R 4.2.0)
##  reticulate         1.28      2023-01-27 [1] CRAN (R 4.2.0)
##  rlang              1.1.1     2023-04-28 [1] CRAN (R 4.2.0)
##  rmarkdown          2.21      2023-03-26 [1] CRAN (R 4.2.0)
##  ROCR               1.0-11    2020-05-02 [2] CRAN (R 4.2.0)
##  rpart              4.1.19    2022-10-21 [1] CRAN (R 4.2.0)
##  Rsamtools          2.14.0    2022-11-01 [1] Bioconductor
##  RSQLite            2.3.1     2023-04-03 [1] CRAN (R 4.2.0)
##  rstudioapi         0.14      2022-08-22 [1] CRAN (R 4.2.0)
##  Rtsne              0.16      2022-04-17 [2] CRAN (R 4.2.0)
##  S4Vectors          0.36.2    2023-02-26 [1] Bioconductor
##  sass               0.4.5     2023-01-24 [1] CRAN (R 4.2.0)
##  scales             1.2.1     2022-08-20 [1] CRAN (R 4.2.0)
##  scattermore        0.8       2022-02-14 [1] CRAN (R 4.2.0)
##  sctransform        0.3.5     2022-09-21 [1] CRAN (R 4.2.0)
##  sessioninfo        1.2.2     2021-12-06 [2] CRAN (R 4.2.0)
##  Seurat           * 4.3.0     2022-11-18 [1] CRAN (R 4.2.0)
##  SeuratObject     * 4.1.3     2022-11-07 [1] CRAN (R 4.2.0)
##  shiny              1.7.4     2022-12-15 [1] CRAN (R 4.2.0)
##  Signac           * 1.9.0     2022-12-08 [1] CRAN (R 4.2.0)
##  sp                 1.6-0     2023-01-19 [1] CRAN (R 4.2.0)
##  spatstat.data      3.0-1     2023-03-12 [1] CRAN (R 4.2.0)
##  spatstat.explore   3.1-0     2023-03-14 [1] CRAN (R 4.2.0)
##  spatstat.geom      3.1-0     2023-03-12 [1] CRAN (R 4.2.0)
##  spatstat.random    3.1-4     2023-03-13 [1] CRAN (R 4.2.0)
##  spatstat.sparse    3.0-1     2023-03-12 [1] CRAN (R 4.2.0)
##  spatstat.utils     3.0-2     2023-03-11 [1] CRAN (R 4.2.0)
##  stringi            1.7.12    2023-01-11 [1] CRAN (R 4.2.0)
##  stringr            1.5.0     2022-12-02 [1] CRAN (R 4.2.0)
##  survival           3.5-5     2023-03-12 [1] CRAN (R 4.2.0)
##  tensor             1.5       2012-05-05 [2] CRAN (R 4.2.0)
##  tibble             3.2.1     2023-03-20 [1] CRAN (R 4.2.0)
##  tidyr              1.3.0     2023-01-24 [1] CRAN (R 4.2.0)
##  tidyselect         1.2.0     2022-10-10 [1] CRAN (R 4.2.0)
##  urlchecker         1.0.1     2021-11-30 [1] CRAN (R 4.2.0)
##  usethis            2.1.6     2022-05-25 [1] CRAN (R 4.2.0)
##  utf8               1.2.3     2023-01-31 [1] CRAN (R 4.2.0)
##  uwot               0.1.14    2022-08-22 [1] CRAN (R 4.2.0)
##  vctrs              0.6.2     2023-04-19 [1] CRAN (R 4.2.0)
##  viridisLite        0.4.2     2023-05-02 [1] CRAN (R 4.2.0)
##  WGCNA            * 1.72-1    2023-01-18 [1] CRAN (R 4.2.0)
##  withr              2.5.0     2022-03-03 [2] CRAN (R 4.2.0)
##  xfun               0.39      2023-04-20 [1] CRAN (R 4.2.0)
##  xtable             1.8-4     2019-04-21 [2] CRAN (R 4.2.0)
##  XVector            0.38.0    2022-11-01 [1] Bioconductor
##  yaml               2.3.7     2023-01-23 [1] CRAN (R 4.2.0)
##  zip                2.3.0     2023-04-17 [1] CRAN (R 4.2.0)
##  zlibbioc           1.44.0    2022-11-01 [1] Bioconductor
##  zoo                1.8-12    2023-04-13 [1] CRAN (R 4.2.0)
## 
##  [1] /gpfs/gibbs/project/ya-chi_ho/jac369/R/4.2
##  [2] /vast/palmer/apps/avx2/software/R/4.2.0-foss-2020b/lib64/R/library
## 
## ------------------------------------------------------------------------------